aboutsummaryrefslogtreecommitdiff
Error: user-error ("Unable to resolve link: \"introduction\"") mapbacktrace(#f(compiled-function (evald func args flags) #)) debug-early-backtrace() debug-early(error (user-error "Unable to resolve link: \"introduction\"")) signal(user-error ("Unable to resolve link: \"introduction\"")) user-error("Unable to resolve link: %S" "introduction") org-export-data((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #126))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #172) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #175))) #126 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #177))) :mode nil :granularity nil :parent #172) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #177) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #180) #("Large system deployments can get very " 0 38 (:parent #183)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #183) #("complex" 0 7 (:parent #187))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #183) #("Guix-notes" 0 10 (:parent #189))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #183))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #180) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #184) #("Guix bioinformatics" 0 19 (:parent #188))) #("and " 0 4 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #180) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #185)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #178) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #181) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #184)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #184)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #184))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #179) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #182) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #185)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #189) #("settings.py" 0 11 (:parent #193)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #185))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #182) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #187))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #182) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #189))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #183) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #186) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #189) #("Note: we moved to MariaDB" 0 25 (:parent #192))) #("\n" 0 1 (:parent #189))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #186) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #190))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #191))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #186) #("If you want to run as root you may have to set\n" 0 47 (:parent #193))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #186) #("You also need to set\n" 0 21 (:parent #195))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #186) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #197))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #186) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #198))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #186) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #200))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #186) #("When you get errors like:\n" 0 26 (:parent #202))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #186) #("you may need to set\n" 0 20 (:parent #204))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #184) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #187) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #190)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #190) #("s" 0 1 (:parent #195))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #190)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #187) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #187) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #187) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #203))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #187) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #204))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #205) #("settings.py" 0 11 (:parent #212))) #("to match your path.\n" 0 20 (:parent #205)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #181) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #184) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #("\n" 0 1 (:parent #188))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #182) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #185) #("See " 0 4 (:parent #188)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #183) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #186) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #189)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #189))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #184))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #187))) :mode section :granularity nil :parent #184) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #187) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #190) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #193)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #193) #("PATH" 0 4 (:parent #197))) #("and R" 0 5 (:parent #193)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #193) #("LIBS" 0 4 (:parent #199))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #193) #("SITE" 0 4 (:parent #200))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #193))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #190) #("On one system:\n" 0 15 (:parent #195))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #190) #("and perhaps a few more.\n" 0 24 (:parent #197))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #188)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #188) #("data" 0 4 (:parent #230))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #188)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #188) #("files" 0 5 (:parent #232))) #("/genotype'" 0 10 (:parent #188))) :mode nil :granularity nil :parent #184) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #188) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #191) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #194)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #194) #("data" 0 4 (:parent #198))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #194)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #194) #("settings.py" 0 11 (:parent #200))) #("(see above in\nthis document).\n" 0 30 (:parent #194))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #191) #("You can use the GENENETWORK" 0 27 (:parent #195)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #195) #("FILES" 0 5 (:parent #199))) #("switch to set the datadir, for example\n" 0 39 (:parent #195))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #191)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #189))) :mode nil :granularity nil :parent #184) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #189) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #192) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #195))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #190))) :mode nil :granularity nil :parent #184) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #190) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #193) #("This error\n" 0 11 (:parent #196))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #193) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #198))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #193) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #199)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #199) #("LIBS" 0 4 (:parent #203))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #199) #("SITE" 0 4 (:parent #204))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #199))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #191))) :mode nil :granularity nil :parent #184) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #191) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #194) #("The following error\n" 0 20 (:parent #197))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #194) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #199))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #194) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #201))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #194) #("if that works run genenetwork after setting SQL" 0 47 (:parent #203)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #203) #("URI" 0 3 (:parent #207))) #("to something like\n" 0 18 (:parent #203))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #194))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #185) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #188) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #191))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #188) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #192))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #188) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #188) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #188) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #188) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #196)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #188) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #188) #(" which should have the same HASH values " 0 48 (:parent #198)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #198) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #202))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #198)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #208))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #209))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #198)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #198)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #213))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #214))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #198)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #216))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #217))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #198))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #82) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #85) #("Install" 0 7 (:parent #88))) #("\n" 0 1 (:parent #85)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #83) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #86) #("Running GN2" 0 11 (:parent #89))) #("\n" 0 1 (:parent #86)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #84) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #87) #("Run MariaDB server" 0 18 (:parent #90))) #("\n" 0 1 (:parent #87))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #84) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #91) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #94) #("Install MariaDB with GNU GUIx" 0 29 (:parent #97))) #("\n" 0 1 (:parent #94)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #92) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #95) #("Load the small database in MySQL" 0 32 (:parent #98))) #("\n" 0 1 (:parent #95)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #85) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #88) #("GN2 Dependency Graph" 0 20 (:parent #91))) #("\n" 0 1 (:parent #88)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #86) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #89) #("Working with the GN2 source code" 0 32 (:parent #92))) #("\n" 0 1 (:parent #89)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #87) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #90) #("Read more" 0 9 (:parent #93))) #("\n" 0 1 (:parent #90)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #88) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #91) #("Trouble shooting" 0 16 (:parent #94))) #("\n" 0 1 (:parent #91))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #88) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #95) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #98) #("ImportError: No module named jinja2" 0 35 (:parent #101))) #("\n" 0 1 (:parent #98)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #96) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #99) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #102)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #102) #("data" 0 4 (:parent #106))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #102)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #102) #("files" 0 5 (:parent #108))) #("/genotype'" 0 10 (:parent #102))) #("\n" 0 1 (:parent #99)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #97) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #100) #("Can't run a module" 0 18 (:parent #103))) #("\n" 0 1 (:parent #100)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #98) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #101) #("Rpy2 error 'show' now found" 0 27 (:parent #104))) #("\n" 0 1 (:parent #101)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #99) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #102) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #105))) #("\n" 0 1 (:parent #102)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #89) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #92) #("IRC session" 0 11 (:parent #95))) #("\n" 0 1 (:parent #92)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #90) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #93) #("NOTES" 0 5 (:parent #96))) #("\n" 0 1 (:parent #93))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #90) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #94) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #97) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #100) #("Deploying GN2 official" 0 22 (:parent #103))) #("\n" 0 1 (:parent #100)))))))) #26)) #0 #("\n" 0 1 (:parent #26)))) #("Introduction" 0 12 (:parent #0))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #126))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #172) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #175))) #126 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #177))) :mode nil :granularity nil :parent #172) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #177) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #180) #("Large system deployments can get very " 0 38 (:parent #183)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #183) #("complex" 0 7 (:parent #187))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #183) #("Guix-notes" 0 10 (:parent #189))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #183))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #180) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #184) #("Guix bioinformatics" 0 19 (:parent #188))) #("and " 0 4 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #180) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #185)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #178) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #181) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #184)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #184)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #184))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #179) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #182) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #185)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #189) #("settings.py" 0 11 (:parent #193)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #185))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #182) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #187))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #182) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #189))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #183) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #186) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #189) #("Note: we moved to MariaDB" 0 25 (:parent #192))) #("\n" 0 1 (:parent #189))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #186) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #190))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #191))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #186) #("If you want to run as root you may have to set\n" 0 47 (:parent #193))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #186) #("You also need to set\n" 0 21 (:parent #195))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #186) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #197))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #186) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #198))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #186) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #200))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #186) #("When you get errors like:\n" 0 26 (:parent #202))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #186) #("you may need to set\n" 0 20 (:parent #204))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #184) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #187) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #190)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #190) #("s" 0 1 (:parent #195))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #190)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #187) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #187) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #187) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #203))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #187) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #204))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #205) #("settings.py" 0 11 (:parent #212))) #("to match your path.\n" 0 20 (:parent #205)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #181) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #184) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #("\n" 0 1 (:parent #188))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #182) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #185) #("See " 0 4 (:parent #188)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #183) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #186) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #189)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #189))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #184))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #187))) :mode section :granularity nil :parent #184) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #187) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #190) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #193)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #193) #("PATH" 0 4 (:parent #197))) #("and R" 0 5 (:parent #193)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #193) #("LIBS" 0 4 (:parent #199))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #193) #("SITE" 0 4 (:parent #200))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #193))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #190) #("On one system:\n" 0 15 (:parent #195))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #190) #("and perhaps a few more.\n" 0 24 (:parent #197))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #188)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #188) #("data" 0 4 (:parent #230))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #188)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #188) #("files" 0 5 (:parent #232))) #("/genotype'" 0 10 (:parent #188))) :mode nil :granularity nil :parent #184) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #188) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #191) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #194)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #194) #("data" 0 4 (:parent #198))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #194)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #194) #("settings.py" 0 11 (:parent #200))) #("(see above in\nthis document).\n" 0 30 (:parent #194))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #191) #("You can use the GENENETWORK" 0 27 (:parent #195)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #195) #("FILES" 0 5 (:parent #199))) #("switch to set the datadir, for example\n" 0 39 (:parent #195))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #191)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #189))) :mode nil :granularity nil :parent #184) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #189) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #192) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #195))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #190))) :mode nil :granularity nil :parent #184) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #190) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #193) #("This error\n" 0 11 (:parent #196))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #193) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #198))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #193) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #199)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #199) #("LIBS" 0 4 (:parent #203))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #199) #("SITE" 0 4 (:parent #204))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #199))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #191))) :mode nil :granularity nil :parent #184) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #191) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #194) #("The following error\n" 0 20 (:parent #197))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #194) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #199))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #194) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #201))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #194)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #194) #("if that works run genenetwork after setting SQL" 0 47 (:parent #203)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #203) #("URI" 0 3 (:parent #207))) #("to something like\n" 0 18 (:parent #203))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #194))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #185) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #188) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #191))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #188) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #192))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #188) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #188) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #188) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #188) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #196)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #188) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #188) #(" which should have the same HASH values " 0 48 (:parent #198)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #198) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #202))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #198)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #208))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #209))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #198)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #198)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #213))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #214))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #198)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #216))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #217))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #198))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #82) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #85) #("Install" 0 7 (:parent #88))) #("\n" 0 1 (:parent #85)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #83) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #86) #("Running GN2" 0 11 (:parent #89))) #("\n" 0 1 (:parent #86)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #84) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #87) #("Run MariaDB server" 0 18 (:parent #90))) #("\n" 0 1 (:parent #87))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #84) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #91) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #94) #("Install MariaDB with GNU GUIx" 0 29 (:parent #97))) #("\n" 0 1 (:parent #94)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #88) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #92) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #95) #("Load the small database in MySQL" 0 32 (:parent #98))) #("\n" 0 1 (:parent #95)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #85) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #88) #("GN2 Dependency Graph" 0 20 (:parent #91))) #("\n" 0 1 (:parent #88)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #86) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #89) #("Working with the GN2 source code" 0 32 (:parent #92))) #("\n" 0 1 (:parent #89)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #87) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #90) #("Read more" 0 9 (:parent #93))) #("\n" 0 1 (:parent #90)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #88) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #91) #("Trouble shooting" 0 16 (:parent #94))) #("\n" 0 1 (:parent #91))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #88) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #95) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #98) #("ImportError: No module named jinja2" 0 35 (:parent #101))) #("\n" 0 1 (:parent #98)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #96) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #99) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #102)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #102) #("data" 0 4 (:parent #106))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #102)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #102) #("files" 0 5 (:parent #108))) #("/genotype'" 0 10 (:parent #102))) #("\n" 0 1 (:parent #99)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #97) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #100) #("Can't run a module" 0 18 (:parent #103))) #("\n" 0 1 (:parent #100)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #98) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #101) #("Rpy2 error 'show' now found" 0 27 (:parent #104))) #("\n" 0 1 (:parent #101)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #92) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #99) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #102) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #105))) #("\n" 0 1 (:parent #102)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #89) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #92) #("IRC session" 0 11 (:parent #95))) #("\n" 0 1 (:parent #92)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #90) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #93) #("NOTES" 0 5 (:parent #96))) #("\n" 0 1 (:parent #93))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #90) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #94) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #97) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #100) #("Deploying GN2 official" 0 22 (:parent #103))) #("\n" 0 1 (:parent #100)))))))) #26)) #0 #("\n" 0 1 (:parent #26)))) #("Introduction" 0 12 (:parent #0)))) mapconcat(#f(compiled-function (element) #) ((link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #127))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #173) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #176))) #127 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #178))) :mode nil :granularity nil :parent #173) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #178) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #181) #("Large system deployments can get very " 0 38 (:parent #184)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #184) #("complex" 0 7 (:parent #188))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #184) #("Guix-notes" 0 10 (:parent #190))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #184))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #181) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #185) #("Guix bioinformatics" 0 19 (:parent #189))) #("and " 0 4 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #185) #("GNU Guix" 0 8 (:parent #191))) #(".\n" 0 2 (:parent #185))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #181) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #186)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #186) #("GN2 Dependency Graph" 0 20 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #179))) :mode nil :granularity nil :parent #173) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #179) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #182) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #185)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #185)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #185))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #180))) :mode nil :granularity nil :parent #173) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #180) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #183) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #186)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #186) #("default" 0 7 (:parent #190)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #190) #("settings.py" 0 11 (:parent #194)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #186))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #183)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #183) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #188))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #183)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #183) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #190))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #181))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #184))) :mode section :granularity nil :parent #181) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #184) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #187) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #190) #("Note: we moved to MariaDB" 0 25 (:parent #193))) #("\n" 0 1 (:parent #190))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #187) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #191))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #187) #("As root configure and run\n" 0 26 (:parent #192))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #187) #("If you want to run as root you may have to set\n" 0 47 (:parent #194))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #187) #("You also need to set\n" 0 21 (:parent #196))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #187) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #198))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #187) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #199))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #187) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #201))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #187) #("When you get errors like:\n" 0 26 (:parent #203))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #187) #("you may need to set\n" 0 20 (:parent #205))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #187)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #185))) :mode nil :granularity nil :parent #181) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #185) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #188) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #191)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #195))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #191) #("s" 0 1 (:parent #196))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #191)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #191) #("plant" 0 5 (:parent #199))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #191))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #188) #("Download one database from\n" 0 27 (:parent #192))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #188) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #188) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #188) #("Check the md5sum.\n" 0 18 (:parent #195))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #188) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #196))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #188) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #198))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #188) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #188) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #188) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #188) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #188) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #206) #("webqtl" 0 6 (:parent #210))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #206) #("s" 0 1 (:parent #211))) #(", or\nchange the settings in etc/default" 0 39 (:parent #206)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #206) #("settings.py" 0 11 (:parent #213))) #("to match your path.\n" 0 20 (:parent #206)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #182))) :mode nil :granularity nil :parent #173) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #182) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #185) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #188))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #185) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #183))) :mode nil :granularity nil :parent #173) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #183) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #186) #("See " 0 4 (:parent #189)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #173) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #184) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #187) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #190)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #190))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #185))) :mode nil :granularity nil :parent #173) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #188) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #191) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #194)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #194) #("PATH" 0 4 (:parent #198))) #("and R" 0 5 (:parent #194)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #194) #("LIBS" 0 4 (:parent #200))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #194) #("SITE" 0 4 (:parent #201))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #194))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #191) #("On one system:\n" 0 15 (:parent #196))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #191) #("and perhaps a few more.\n" 0 24 (:parent #198))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #189)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #189) #("data" 0 4 (:parent #231))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #189)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #189) #("files" 0 5 (:parent #233))) #("/genotype'" 0 10 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #189) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #192) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #195)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #195) #("data" 0 4 (:parent #199))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #195)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #195) #("settings.py" 0 11 (:parent #201))) #("(see above in\nthis document).\n" 0 30 (:parent #195))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #192) #("You can use the GENENETWORK" 0 27 (:parent #196)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #196) #("FILES" 0 5 (:parent #200))) #("switch to set the datadir, for example\n" 0 39 (:parent #196))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #192)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #190))) :mode nil :granularity nil :parent #185) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #190) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #193) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #196))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #191))) :mode nil :granularity nil :parent #185) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #191) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #194) #("This error\n" 0 11 (:parent #197))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #194)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #194) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #199))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #194) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #200)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #200) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #200) #("SITE" 0 4 (:parent #205))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #200))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #192))) :mode nil :granularity nil :parent #185) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #192) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #195) #("The following error\n" 0 20 (:parent #198))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #195) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #200))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #195) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #202))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #195) #("if that works run genenetwork after setting SQL" 0 47 (:parent #204)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #204) #("URI" 0 3 (:parent #208))) #("to something like\n" 0 18 (:parent #204))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #195))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #186))) :mode nil :granularity nil :parent #173) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #186) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #189) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #192))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #193))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #189) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #189) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #189) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #196))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #189) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #197)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #197))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #189) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #198))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #189) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #199) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #203))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #199)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #199)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #199)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #209))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #210))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #199)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #199)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #214))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #215))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #199)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #217))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #218))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #199))))))) #103)) #79)) #47 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #83) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #86) #("Install" 0 7 (:parent #89))) #("\n" 0 1 (:parent #86)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #84) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #87) #("Running GN2" 0 11 (:parent #90))) #("\n" 0 1 (:parent #87)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #85) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #88) #("Run MariaDB server" 0 18 (:parent #91))) #("\n" 0 1 (:parent #88))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #85) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #92) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #95) #("Install MariaDB with GNU GUIx" 0 29 (:parent #98))) #("\n" 0 1 (:parent #95)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #93) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #96) #("Load the small database in MySQL" 0 32 (:parent #99))) #("\n" 0 1 (:parent #96)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #86) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #89) #("GN2 Dependency Graph" 0 20 (:parent #92))) #("\n" 0 1 (:parent #89)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #87) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #90) #("Working with the GN2 source code" 0 32 (:parent #93))) #("\n" 0 1 (:parent #90)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #88) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #91) #("Read more" 0 9 (:parent #94))) #("\n" 0 1 (:parent #91)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #89) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #92) #("Trouble shooting" 0 16 (:parent #95))) #("\n" 0 1 (:parent #92))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #89) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #93) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #96) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #99) #("ImportError: No module named jinja2" 0 35 (:parent #102))) #("\n" 0 1 (:parent #99)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #93) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #97) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #100) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #103)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #103) #("data" 0 4 (:parent #107))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #103)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #103) #("files" 0 5 (:parent #109))) #("/genotype'" 0 10 (:parent #103))) #("\n" 0 1 (:parent #100)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #93) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #98) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #101) #("Can't run a module" 0 18 (:parent #104))) #("\n" 0 1 (:parent #101)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #93) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #99) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #102) #("Rpy2 error 'show' now found" 0 27 (:parent #105))) #("\n" 0 1 (:parent #102)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #93) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #100) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #103) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #106))) #("\n" 0 1 (:parent #103)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #90) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #93) #("IRC session" 0 11 (:parent #96))) #("\n" 0 1 (:parent #93)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #91) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #94) #("NOTES" 0 5 (:parent #97))) #("\n" 0 1 (:parent #94))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #91) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #95) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #98) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #101) #("Deploying GN2 official" 0 22 (:parent #104))) #("\n" 0 1 (:parent #101)))))))) #27)) . #0)) #("Introduction" 0 12 (:parent #1))) #("\n" 0 1 (:parent (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #105))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #151) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #154))) #105 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #156) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #159) #("Large system deployments can get very " 0 38 (:parent #162)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #162) #("complex" 0 7 (:parent #166))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #162) #("Guix-notes" 0 10 (:parent #168))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #162))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #159) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #163) #("Guix bioinformatics" 0 19 (:parent #167))) #("and " 0 4 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #163) #("GNU Guix" 0 8 (:parent #169))) #(".\n" 0 2 (:parent #163))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #159) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #164)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #164) #("GN2 Dependency Graph" 0 20 (:parent #168))) #(".\n" 0 2 (:parent #164))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #157) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #160) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #163)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #163)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #163))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #158) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #161) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #164)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #164) #("default" 0 7 (:parent #168)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #168) #("settings.py" 0 11 (:parent #172)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #164))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #161)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #161) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #166))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #161)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #161) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #168))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #159))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #162))) :mode section :granularity nil :parent #159) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #162) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #165) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #168) #("Note: we moved to MariaDB" 0 25 (:parent #171))) #("\n" 0 1 (:parent #168))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #165) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #169))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #165) #("As root configure and run\n" 0 26 (:parent #170))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #165)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #165) #("If you want to run as root you may have to set\n" 0 47 (:parent #172))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #165)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #165) #("You also need to set\n" 0 21 (:parent #174))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #165)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #165) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #176))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #165) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #177))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #165)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #165) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #179))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #165)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #165) #("When you get errors like:\n" 0 26 (:parent #181))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #165)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #165) #("you may need to set\n" 0 20 (:parent #183))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #163))) :mode nil :granularity nil :parent #159) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #163) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #166) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #169)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #169)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #176))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #169) #("plant" 0 5 (:parent #177))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #169))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #166) #("Download one database from\n" 0 27 (:parent #170))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #166) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #171)) #("\n" 0 1 (:parent #171))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #166) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n" 0 1 (:parent #172))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #166) #("Check the md5sum.\n" 0 18 (:parent #173))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #166) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #174))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #166)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #166) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #176))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #166)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #166) #("and\n" 0 4 (:parent #178))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #166)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #166) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #180))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #166)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #166) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #182))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #166) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #183))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #166) #("Note for the plant database you can rename it to db" 0 51 (:parent #184)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #184) #("webqtl" 0 6 (:parent #188))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #184) #("s" 0 1 (:parent #189))) #(", or\nchange the settings in etc/default" 0 39 (:parent #184)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #184) #("settings.py" 0 11 (:parent #191))) #("to match your path.\n" 0 20 (:parent #184)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #160))) :mode nil :granularity nil :parent #151) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #160) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #163) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #166))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #163) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #161))) :mode nil :granularity nil :parent #151) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #161) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #164) #("See " 0 4 (:parent #167)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(".\n" 0 2 (:parent #167))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #162))) :mode nil :granularity nil :parent #151) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #162) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #165) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #168)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #168))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #163))) :mode nil :granularity nil :parent #151) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #166))) :mode section :granularity nil :parent #163) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #166) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #169) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #172)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #172) #("PATH" 0 4 (:parent #176))) #("and R" 0 5 (:parent #172)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #172) #("LIBS" 0 4 (:parent #178))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #172) #("SITE" 0 4 (:parent #179))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #172))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #169)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #169) #("On one system:\n" 0 15 (:parent #174))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #169)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #169) #("and perhaps a few more.\n" 0 24 (:parent #176))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #167)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #167) #("data" 0 4 (:parent #209))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #167)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #167) #("files" 0 5 (:parent #211))) #("/genotype'" 0 10 (:parent #167))) :mode nil :granularity nil :parent #163) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #167) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #170) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #173)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #173) #("data" 0 4 (:parent #177))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #173)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #173) #("settings.py" 0 11 (:parent #179))) #("(see above in\nthis document).\n" 0 30 (:parent #173))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #170) #("You can use the GENENETWORK" 0 27 (:parent #174)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #174) #("FILES" 0 5 (:parent #178))) #("switch to set the datadir, for example\n" 0 39 (:parent #174))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #170)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #168))) :mode nil :granularity nil :parent #163) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #168) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #171) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #174))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #169))) :mode nil :granularity nil :parent #163) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #169) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #172) #("This error\n" 0 11 (:parent #175))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #172)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #172) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #177))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #172) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #178)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #178) #("LIBS" 0 4 (:parent #182))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #178) #("SITE" 0 4 (:parent #183))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #178))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #170))) :mode nil :granularity nil :parent #163) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #170) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #173) #("The following error\n" 0 20 (:parent #176))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #173)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #173) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #178))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #173)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #173) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #180))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #173)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #173) #("if that works run genenetwork after setting SQL" 0 47 (:parent #182)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #182) #("URI" 0 3 (:parent #186))) #("to something like\n" 0 18 (:parent #182))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #173))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #164))) :mode nil :granularity nil :parent #151) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #164) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #167) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #170))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #167) #("#+begin" 0 7 (:parent #171)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #171) #("src" 0 3 (:parent #175))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #171))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #167) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #172))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #167) #(" yes\n env GUIX" 0 30 (:parent #173)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #173))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #167) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #174))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #167) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #175)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #175) #("PACKAGE" 0 7 (:parent #179))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #175) #("PATH" 0 4 (:parent #180))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #175))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #167) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #176))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #167) #(" which should have the same HASH values " 0 48 (:parent #177)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #177) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #181))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #177)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #177)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #177)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #177)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #177)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #192))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #193))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #177)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #177) #("PACKAGE" 0 7 (:parent #195))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #177) #("PATH" 0 4 (:parent #196))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #177)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #177)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #177))))))) #81)) #57)) #25 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #61) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #64) #("Install" 0 7 (:parent #67))) #("\n" 0 1 (:parent #64)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #62) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #65) #("Running GN2" 0 11 (:parent #68))) #("\n" 0 1 (:parent #65)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #63) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #66) #("Run MariaDB server" 0 18 (:parent #69))) #("\n" 0 1 (:parent #66))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #63) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #70) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #73) #("Install MariaDB with GNU GUIx" 0 29 (:parent #76))) #("\n" 0 1 (:parent #73)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #74) #("Load the small database in MySQL" 0 32 (:parent #77))) #("\n" 0 1 (:parent #74)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #64) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #67) #("GN2 Dependency Graph" 0 20 (:parent #70))) #("\n" 0 1 (:parent #67)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #65) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #68) #("Working with the GN2 source code" 0 32 (:parent #71))) #("\n" 0 1 (:parent #68)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #66) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #69) #("Read more" 0 9 (:parent #72))) #("\n" 0 1 (:parent #69)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #67) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #70) #("Trouble shooting" 0 16 (:parent #73))) #("\n" 0 1 (:parent #70))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #67) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #71) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #74) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #77) #("ImportError: No module named jinja2" 0 35 (:parent #80))) #("\n" 0 1 (:parent #77)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #71) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #75) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #78) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #81)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #81) #("data" 0 4 (:parent #85))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #81)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #81) #("files" 0 5 (:parent #87))) #("/genotype'" 0 10 (:parent #81))) #("\n" 0 1 (:parent #78)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #71) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #76) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #79) #("Can't run a module" 0 18 (:parent #82))) #("\n" 0 1 (:parent #79)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #71) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #77) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #80) #("Rpy2 error 'show' now found" 0 27 (:parent #83))) #("\n" 0 1 (:parent #80)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #71) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #78) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #81) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #84))) #("\n" 0 1 (:parent #81)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #68) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #71) #("IRC session" 0 11 (:parent #74))) #("\n" 0 1 (:parent #71)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #57) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #69) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #72) #("NOTES" 0 5 (:parent #75))) #("\n" 0 1 (:parent #72))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #69) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #73) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #76) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #79) #("Deploying GN2 official" 0 22 (:parent #82))) #("\n" 0 1 (:parent #79)))))))) #5)) . #0)))) "") org-export-data((paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #100))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #146) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #149))) #100 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #151) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #154) #("Large system deployments can get very " 0 38 (:parent #157)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #157) #("complex" 0 7 (:parent #161))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #163))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #158) #("GNU Guix" 0 8 (:parent #164))) #(".\n" 0 2 (:parent #158))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #154) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #159)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #159) #("GN2 Dependency Graph" 0 20 (:parent #163))) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #152) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #155) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #158)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #158))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #153) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #156) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #159)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #159) #("default" 0 7 (:parent #163)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #163) #("settings.py" 0 11 (:parent #167)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #159))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #156) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #161))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #156) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #163))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #154))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #157))) :mode section :granularity nil :parent #154) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #157) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #160) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #163) #("Note: we moved to MariaDB" 0 25 (:parent #166))) #("\n" 0 1 (:parent #163))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #160) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #164))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #160) #("As root configure and run\n" 0 26 (:parent #165))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #160) #("If you want to run as root you may have to set\n" 0 47 (:parent #167))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #160) #("You also need to set\n" 0 21 (:parent #169))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #160) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #171))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #160) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #172))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #160) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #174))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #160) #("When you get errors like:\n" 0 26 (:parent #176))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #160)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #160) #("you may need to set\n" 0 20 (:parent #178))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #158))) :mode nil :granularity nil :parent #154) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #158) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #161) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #164)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #164) #("s" 0 1 (:parent #169))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #164)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #164) #("plant" 0 5 (:parent #172))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #164))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #161) #("Download one database from\n" 0 27 (:parent #165))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #161) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #("\n" 0 1 (:parent #166))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #161) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #161) #("Check the md5sum.\n" 0 18 (:parent #168))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #161) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #169))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #161)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #161) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #171))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #161)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #161) #("and\n" 0 4 (:parent #173))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #161)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #161) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #175))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #161)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #161) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #177))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #161) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #178))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #161) #("Note for the plant database you can rename it to db" 0 51 (:parent #179)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #179) #("webqtl" 0 6 (:parent #183))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #179) #("s" 0 1 (:parent #184))) #(", or\nchange the settings in etc/default" 0 39 (:parent #179)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #179) #("settings.py" 0 11 (:parent #186))) #("to match your path.\n" 0 20 (:parent #179)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #155) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #158) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #161))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #158) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n" 0 1 (:parent #162))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #156))) :mode nil :granularity nil :parent #146) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #156) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #159) #("See " 0 4 (:parent #162)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #(".\n" 0 2 (:parent #162))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #157) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #160) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #163)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #163))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #158))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #161))) :mode section :granularity nil :parent #158) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #161) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #164) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #167)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #167) #("PATH" 0 4 (:parent #171))) #("and R" 0 5 (:parent #167)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #167) #("LIBS" 0 4 (:parent #173))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #167) #("SITE" 0 4 (:parent #174))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #167))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #164) #("On one system:\n" 0 15 (:parent #169))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #164) #("and perhaps a few more.\n" 0 24 (:parent #171))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #162)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #162) #("data" 0 4 (:parent #204))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #162)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #162) #("files" 0 5 (:parent #206))) #("/genotype'" 0 10 (:parent #162))) :mode nil :granularity nil :parent #158) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #162) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #165) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #168)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #168) #("data" 0 4 (:parent #172))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #168)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #168) #("settings.py" 0 11 (:parent #174))) #("(see above in\nthis document).\n" 0 30 (:parent #168))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #165) #("You can use the GENENETWORK" 0 27 (:parent #169)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #169) #("FILES" 0 5 (:parent #173))) #("switch to set the datadir, for example\n" 0 39 (:parent #169))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #163))) :mode nil :granularity nil :parent #158) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #163) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #166) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #169))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #164))) :mode nil :granularity nil :parent #158) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #164) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #167) #("This error\n" 0 11 (:parent #170))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #167) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #172))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #167) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #173)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #173) #("LIBS" 0 4 (:parent #177))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #173) #("SITE" 0 4 (:parent #178))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #173))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #165))) :mode nil :granularity nil :parent #158) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #165) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #168) #("The following error\n" 0 20 (:parent #171))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #168) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #173))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #168) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #175))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #168) #("if that works run genenetwork after setting SQL" 0 47 (:parent #177)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #177) #("URI" 0 3 (:parent #181))) #("to something like\n" 0 18 (:parent #177))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #168))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #159) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #162) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #165))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #162) #("#+begin" 0 7 (:parent #166)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #166) #("src" 0 3 (:parent #170))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #166))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #162) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #167))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #162) #(" yes\n env GUIX" 0 30 (:parent #168)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #168) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #168) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #168))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #162) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #169))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #162) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #170)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #170) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #170) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #170))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #162) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #171))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #162) #(" which should have the same HASH values " 0 48 (:parent #172)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #172) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #176))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #172)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #182))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #183))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #172)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #172)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #172)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #190))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #191))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #172))))))) #76)) #52)) #20 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #56) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #59) #("Install" 0 7 (:parent #62))) #("\n" 0 1 (:parent #59)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #57) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #60) #("Running GN2" 0 11 (:parent #63))) #("\n" 0 1 (:parent #60)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #58) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #61) #("Run MariaDB server" 0 18 (:parent #64))) #("\n" 0 1 (:parent #61))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #58) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #62) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #65) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #68) #("Install MariaDB with GNU GUIx" 0 29 (:parent #71))) #("\n" 0 1 (:parent #68)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #62) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #66) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #69) #("Load the small database in MySQL" 0 32 (:parent #72))) #("\n" 0 1 (:parent #69)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #59) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #62) #("GN2 Dependency Graph" 0 20 (:parent #65))) #("\n" 0 1 (:parent #62)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #60) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #63) #("Working with the GN2 source code" 0 32 (:parent #66))) #("\n" 0 1 (:parent #63)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #61) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #64) #("Read more" 0 9 (:parent #67))) #("\n" 0 1 (:parent #64)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #62) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #65) #("Trouble shooting" 0 16 (:parent #68))) #("\n" 0 1 (:parent #65))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #62) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #69) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #72) #("ImportError: No module named jinja2" 0 35 (:parent #75))) #("\n" 0 1 (:parent #72)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #70) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #73) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #76)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #76) #("data" 0 4 (:parent #80))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #76)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #76) #("files" 0 5 (:parent #82))) #("/genotype'" 0 10 (:parent #76))) #("\n" 0 1 (:parent #73)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #74) #("Can't run a module" 0 18 (:parent #77))) #("\n" 0 1 (:parent #74)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #72) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #75) #("Rpy2 error 'show' now found" 0 27 (:parent #78))) #("\n" 0 1 (:parent #75)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #73) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #76) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #79))) #("\n" 0 1 (:parent #76)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #63) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #66) #("IRC session" 0 11 (:parent #69))) #("\n" 0 1 (:parent #66)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #64) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #67) #("NOTES" 0 5 (:parent #70))) #("\n" 0 1 (:parent #67))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #64) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #68) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #74) #("Deploying GN2 official" 0 22 (:parent #77))) #("\n" 0 1 (:parent #74)))))))) #0)) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #0) #("Introduction" 0 12 (:parent #3))) #("\n" 0 1 (:parent #0))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #100))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #146) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #149))) #100 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #151) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #154) #("Large system deployments can get very " 0 38 (:parent #157)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #157) #("complex" 0 7 (:parent #161))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #163))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #158) #("GNU Guix" 0 8 (:parent #164))) #(".\n" 0 2 (:parent #158))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #154) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #159)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #159) #("GN2 Dependency Graph" 0 20 (:parent #163))) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #152) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #155) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #158)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #158))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #153) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #156) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #159)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #159) #("default" 0 7 (:parent #163)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #163) #("settings.py" 0 11 (:parent #167)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #159))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #156) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #161))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #156) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #163))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #154))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #157))) :mode section :granularity nil :parent #154) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #157) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #160) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #163) #("Note: we moved to MariaDB" 0 25 (:parent #166))) #("\n" 0 1 (:parent #163))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #160) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #164))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #160) #("As root configure and run\n" 0 26 (:parent #165))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #160) #("If you want to run as root you may have to set\n" 0 47 (:parent #167))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #160) #("You also need to set\n" 0 21 (:parent #169))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #160) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #171))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #160) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #172))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #160) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #174))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #160)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #160) #("When you get errors like:\n" 0 26 (:parent #176))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #160)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #160) #("you may need to set\n" 0 20 (:parent #178))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #158))) :mode nil :granularity nil :parent #154) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #158) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #161) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #164)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #164) #("s" 0 1 (:parent #169))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #164)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #164) #("plant" 0 5 (:parent #172))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #164))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #161) #("Download one database from\n" 0 27 (:parent #165))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #161) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #("\n" 0 1 (:parent #166))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #161) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #161) #("Check the md5sum.\n" 0 18 (:parent #168))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #161) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #169))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #161)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #161) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #171))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #161)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #161) #("and\n" 0 4 (:parent #173))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #161)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #161) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #175))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #161)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #161) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #177))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #161) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #178))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #161) #("Note for the plant database you can rename it to db" 0 51 (:parent #179)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #179) #("webqtl" 0 6 (:parent #183))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #179) #("s" 0 1 (:parent #184))) #(", or\nchange the settings in etc/default" 0 39 (:parent #179)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #179) #("settings.py" 0 11 (:parent #186))) #("to match your path.\n" 0 20 (:parent #179)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #155) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #158) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #161))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #158) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n" 0 1 (:parent #162))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #156))) :mode nil :granularity nil :parent #146) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #156) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #159) #("See " 0 4 (:parent #162)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #(".\n" 0 2 (:parent #162))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #157) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #160) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #163)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #163))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #158))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #161))) :mode section :granularity nil :parent #158) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #161) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #164) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #167)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #167) #("PATH" 0 4 (:parent #171))) #("and R" 0 5 (:parent #167)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #167) #("LIBS" 0 4 (:parent #173))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #167) #("SITE" 0 4 (:parent #174))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #167))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #164) #("On one system:\n" 0 15 (:parent #169))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #164) #("and perhaps a few more.\n" 0 24 (:parent #171))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #162)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #162) #("data" 0 4 (:parent #204))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #162)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #162) #("files" 0 5 (:parent #206))) #("/genotype'" 0 10 (:parent #162))) :mode nil :granularity nil :parent #158) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #162) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #165) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #168)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #168) #("data" 0 4 (:parent #172))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #168)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #168) #("settings.py" 0 11 (:parent #174))) #("(see above in\nthis document).\n" 0 30 (:parent #168))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #165) #("You can use the GENENETWORK" 0 27 (:parent #169)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #169) #("FILES" 0 5 (:parent #173))) #("switch to set the datadir, for example\n" 0 39 (:parent #169))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #163))) :mode nil :granularity nil :parent #158) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #163) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #166) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #169))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #164))) :mode nil :granularity nil :parent #158) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #164) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #167) #("This error\n" 0 11 (:parent #170))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #167) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #172))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #167) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #173)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #173) #("LIBS" 0 4 (:parent #177))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #173) #("SITE" 0 4 (:parent #178))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #173))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #165))) :mode nil :granularity nil :parent #158) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #165) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #168) #("The following error\n" 0 20 (:parent #171))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #168) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #173))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #168) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #175))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #168)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #168) #("if that works run genenetwork after setting SQL" 0 47 (:parent #177)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #177) #("URI" 0 3 (:parent #181))) #("to something like\n" 0 18 (:parent #177))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #168))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #159) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #162) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #165))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #162) #("#+begin" 0 7 (:parent #166)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #166) #("src" 0 3 (:parent #170))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #166))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #162) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #167))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #162) #(" yes\n env GUIX" 0 30 (:parent #168)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #168) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #168) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #168))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #162) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #169))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #162) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #170)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #170) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #170) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #170))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #162) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #171))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #162) #(" which should have the same HASH values " 0 48 (:parent #172)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #172) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #176))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #172)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #172)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #172)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #182))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #183))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #172)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #172)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #187))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #188))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #172)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #172) #("PACKAGE" 0 7 (:parent #190))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #172) #("PATH" 0 4 (:parent #191))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #172)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #172))))))) #76)) #52)) #20 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #56) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #59) #("Install" 0 7 (:parent #62))) #("\n" 0 1 (:parent #59)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #57) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #60) #("Running GN2" 0 11 (:parent #63))) #("\n" 0 1 (:parent #60)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #58) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #61) #("Run MariaDB server" 0 18 (:parent #64))) #("\n" 0 1 (:parent #61))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #58) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #62) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #65) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #68) #("Install MariaDB with GNU GUIx" 0 29 (:parent #71))) #("\n" 0 1 (:parent #68)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #62) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #66) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #69) #("Load the small database in MySQL" 0 32 (:parent #72))) #("\n" 0 1 (:parent #69)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #59) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #62) #("GN2 Dependency Graph" 0 20 (:parent #65))) #("\n" 0 1 (:parent #62)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #60) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #63) #("Working with the GN2 source code" 0 32 (:parent #66))) #("\n" 0 1 (:parent #63)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #61) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #64) #("Read more" 0 9 (:parent #67))) #("\n" 0 1 (:parent #64)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #62) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #65) #("Trouble shooting" 0 16 (:parent #68))) #("\n" 0 1 (:parent #65))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #62) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #69) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #72) #("ImportError: No module named jinja2" 0 35 (:parent #75))) #("\n" 0 1 (:parent #72)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #70) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #73) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #76)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #76) #("data" 0 4 (:parent #80))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #76)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #76) #("files" 0 5 (:parent #82))) #("/genotype'" 0 10 (:parent #76))) #("\n" 0 1 (:parent #73)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #74) #("Can't run a module" 0 18 (:parent #77))) #("\n" 0 1 (:parent #74)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #72) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #75) #("Rpy2 error 'show' now found" 0 27 (:parent #78))) #("\n" 0 1 (:parent #75)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #66) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #73) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #76) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #79))) #("\n" 0 1 (:parent #76)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #63) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #66) #("IRC session" 0 11 (:parent #69))) #("\n" 0 1 (:parent #66)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #52) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #64) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #67) #("NOTES" 0 5 (:parent #70))) #("\n" 0 1 (:parent #67))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #64) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #68) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #74) #("Deploying GN2 official" 0 22 (:parent #77))) #("\n" 0 1 (:parent #74)))))))) #0)) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #0) #("Introduction" 0 12 (:parent #3))) #("\n" 0 1 (:parent #0)))) mapconcat(#f(compiled-function (element) #) ((paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #101))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #147) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #150))) #101 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #152) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #155) #("Large system deployments can get very " 0 38 (:parent #158)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #158) #("complex" 0 7 (:parent #162))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #158) #("Guix-notes" 0 10 (:parent #164))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #158))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #155) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #159) #("Guix bioinformatics" 0 19 (:parent #163))) #("and " 0 4 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #159) #("GNU Guix" 0 8 (:parent #165))) #(".\n" 0 2 (:parent #159))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #155) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #160)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #160) #("GN2 Dependency Graph" 0 20 (:parent #164))) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #153) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #156) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #159)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #159))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #154) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #157) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #160)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #160) #("default" 0 7 (:parent #164)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #164) #("settings.py" 0 11 (:parent #168)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #160))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #157)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #157) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #162))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #157)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #157) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #164))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #155))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #158))) :mode section :granularity nil :parent #155) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #158) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #161) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #164) #("Note: we moved to MariaDB" 0 25 (:parent #167))) #("\n" 0 1 (:parent #164))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #161) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #165))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #161) #("As root configure and run\n" 0 26 (:parent #166))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #161) #("If you want to run as root you may have to set\n" 0 47 (:parent #168))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #161) #("You also need to set\n" 0 21 (:parent #170))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #161) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #172))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #161) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #173))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #161) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #175))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #161) #("When you get errors like:\n" 0 26 (:parent #177))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #161)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #161) #("you may need to set\n" 0 20 (:parent #179))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #161)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #159))) :mode nil :granularity nil :parent #155) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #159) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #162) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #165)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #165) #("webqtl" 0 6 (:parent #169))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #165) #("s" 0 1 (:parent #170))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #165)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #165) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #165) #("plant" 0 5 (:parent #173))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #165))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #162) #("Download one database from\n" 0 27 (:parent #166))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #162) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #162) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\n" 0 1 (:parent #168))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #162) #("Check the md5sum.\n" 0 18 (:parent #169))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #162) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #170))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #162) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #172))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #162) #("and\n" 0 4 (:parent #174))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #162)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #162) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #176))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #162)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #162) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #178))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #162) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #179))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #162) #("Note for the plant database you can rename it to db" 0 51 (:parent #180)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #180) #("webqtl" 0 6 (:parent #184))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #180) #("s" 0 1 (:parent #185))) #(", or\nchange the settings in etc/default" 0 39 (:parent #180)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #180) #("settings.py" 0 11 (:parent #187))) #("to match your path.\n" 0 20 (:parent #180)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #156))) :mode nil :granularity nil :parent #147) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #156) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #159) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #162))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #159) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\n" 0 1 (:parent #163))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #157))) :mode nil :granularity nil :parent #147) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #157) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #160) #("See " 0 4 (:parent #163)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #(".\n" 0 2 (:parent #163))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #158))) :mode nil :granularity nil :parent #147) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #158) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #161) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #164)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #164)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #164))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #159))) :mode nil :granularity nil :parent #147) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #162))) :mode section :granularity nil :parent #159) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #162) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #165) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #168)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #168) #("PATH" 0 4 (:parent #172))) #("and R" 0 5 (:parent #168)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #168) #("LIBS" 0 4 (:parent #174))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #168) #("SITE" 0 4 (:parent #175))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #168))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #165)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #165) #("On one system:\n" 0 15 (:parent #170))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #165)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #165) #("and perhaps a few more.\n" 0 24 (:parent #172))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #163)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #163) #("data" 0 4 (:parent #205))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #163)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #163) #("files" 0 5 (:parent #207))) #("/genotype'" 0 10 (:parent #163))) :mode nil :granularity nil :parent #159) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #163) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #166) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #169)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #169) #("data" 0 4 (:parent #173))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #169)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #169) #("settings.py" 0 11 (:parent #175))) #("(see above in\nthis document).\n" 0 30 (:parent #169))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #166) #("You can use the GENENETWORK" 0 27 (:parent #170)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #170) #("FILES" 0 5 (:parent #174))) #("switch to set the datadir, for example\n" 0 39 (:parent #170))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #166)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #164))) :mode nil :granularity nil :parent #159) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #164) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #167) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #170))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #165))) :mode nil :granularity nil :parent #159) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #165) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #168) #("This error\n" 0 11 (:parent #171))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #168)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #168) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #173))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #168) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #174)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #174) #("LIBS" 0 4 (:parent #178))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #174) #("SITE" 0 4 (:parent #179))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #174))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #166))) :mode nil :granularity nil :parent #159) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #166) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #169) #("The following error\n" 0 20 (:parent #172))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #169)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #169) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #174))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #169)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #169) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #176))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #169)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #169) #("if that works run genenetwork after setting SQL" 0 47 (:parent #178)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #178) #("URI" 0 3 (:parent #182))) #("to something like\n" 0 18 (:parent #178))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #169))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #160))) :mode nil :granularity nil :parent #147) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #160) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #163) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #166))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #163) #("#+begin" 0 7 (:parent #167)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #167) #("src" 0 3 (:parent #171))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #167))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #163) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #168))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #163) #(" yes\n env GUIX" 0 30 (:parent #169)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #169) #("PACKAGE" 0 7 (:parent #173))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #169) #("PATH" 0 4 (:parent #174))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #169))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #163) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #170))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #163) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #171)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #171) #("PACKAGE" 0 7 (:parent #175))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #171) #("PATH" 0 4 (:parent #176))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #171))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #163) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #172))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #163) #(" which should have the same HASH values " 0 48 (:parent #173)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #173) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #177))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #173)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #173)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #173)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #183))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #184))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #173)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #173)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #188))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #189))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #173)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #173) #("PACKAGE" 0 7 (:parent #191))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #173) #("PATH" 0 4 (:parent #192))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #173))))))) #77)) #53)) #21 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #57) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #60) #("Install" 0 7 (:parent #63))) #("\n" 0 1 (:parent #60)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #58) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #61) #("Running GN2" 0 11 (:parent #64))) #("\n" 0 1 (:parent #61)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #59) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #62) #("Run MariaDB server" 0 18 (:parent #65))) #("\n" 0 1 (:parent #62))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #59) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #63) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #66) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #69) #("Install MariaDB with GNU GUIx" 0 29 (:parent #72))) #("\n" 0 1 (:parent #69)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #63) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #67) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #70) #("Load the small database in MySQL" 0 32 (:parent #73))) #("\n" 0 1 (:parent #70)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #60) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #63) #("GN2 Dependency Graph" 0 20 (:parent #66))) #("\n" 0 1 (:parent #63)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #61) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #64) #("Working with the GN2 source code" 0 32 (:parent #67))) #("\n" 0 1 (:parent #64)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #62) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #65) #("Read more" 0 9 (:parent #68))) #("\n" 0 1 (:parent #65)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #63) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #66) #("Trouble shooting" 0 16 (:parent #69))) #("\n" 0 1 (:parent #66))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #63) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #70) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #73) #("ImportError: No module named jinja2" 0 35 (:parent #76))) #("\n" 0 1 (:parent #73)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #71) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #74) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #77)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #77) #("data" 0 4 (:parent #81))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #77)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #77) #("files" 0 5 (:parent #83))) #("/genotype'" 0 10 (:parent #77))) #("\n" 0 1 (:parent #74)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #72) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #75) #("Can't run a module" 0 18 (:parent #78))) #("\n" 0 1 (:parent #75)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #73) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #76) #("Rpy2 error 'show' now found" 0 27 (:parent #79))) #("\n" 0 1 (:parent #76)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #67) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #74) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #77) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #80))) #("\n" 0 1 (:parent #77)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #64) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #67) #("IRC session" 0 11 (:parent #70))) #("\n" 0 1 (:parent #67)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #53) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #65) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #68) #("NOTES" 0 5 (:parent #71))) #("\n" 0 1 (:parent #68))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #65) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #69) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #72) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #75) #("Deploying GN2 official" 0 22 (:parent #78))) #("\n" 0 1 (:parent #75)))))))) . #0)) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #1) #("Introduction" 0 12 (:parent #4))) #("\n" 0 1 (:parent #1)))) "") org-export-data((item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #80))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #126) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #129))) #80 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #131))) :mode nil :granularity nil :parent #126) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #131) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #134) #("Large system deployments can get very " 0 38 (:parent #137)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #137) #("complex" 0 7 (:parent #141))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #143))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #138) #("GNU Guix" 0 8 (:parent #144))) #(".\n" 0 2 (:parent #138))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #134) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #139)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #139) #("GN2 Dependency Graph" 0 20 (:parent #143))) #(".\n" 0 2 (:parent #139))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #132))) :mode nil :granularity nil :parent #126) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #132) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #135) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #138)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #138)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #138))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #133) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #136) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #139)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #139) #("default" 0 7 (:parent #143)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #143) #("settings.py" 0 11 (:parent #147)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #139))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #136) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #141))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #136) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #143))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #134))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #137))) :mode section :granularity nil :parent #134) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #137) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #140) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #143) #("Note: we moved to MariaDB" 0 25 (:parent #146))) #("\n" 0 1 (:parent #143))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #140) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #144))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #140) #("As root configure and run\n" 0 26 (:parent #145))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #140) #("If you want to run as root you may have to set\n" 0 47 (:parent #147))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #140) #("You also need to set\n" 0 21 (:parent #149))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #140) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #151))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #140) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #152))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #140) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #154))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #140) #("When you get errors like:\n" 0 26 (:parent #156))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #140)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #140) #("you may need to set\n" 0 20 (:parent #158))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #138))) :mode nil :granularity nil :parent #134) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #138) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #141) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #144)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #144) #("webqtl" 0 6 (:parent #148))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #144) #("s" 0 1 (:parent #149))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #144)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #144) #("webqtl" 0 6 (:parent #151))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #144) #("plant" 0 5 (:parent #152))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #144))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #141) #("Download one database from\n" 0 27 (:parent #145))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #141) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #141) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #141) #("Check the md5sum.\n" 0 18 (:parent #148))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #141) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #149))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #141) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #151))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #141) #("and\n" 0 4 (:parent #153))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #141) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #155))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #141) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #157))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #141) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #158))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #141) #("Note for the plant database you can rename it to db" 0 51 (:parent #159)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #159) #("webqtl" 0 6 (:parent #163))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #159) #("s" 0 1 (:parent #164))) #(", or\nchange the settings in etc/default" 0 39 (:parent #159)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #159) #("settings.py" 0 11 (:parent #166))) #("to match your path.\n" 0 20 (:parent #159)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #135) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #138) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #141))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #138) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #142)) #("\n" 0 1 (:parent #142))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #136))) :mode nil :granularity nil :parent #126) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #136) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #139) #("See " 0 4 (:parent #142)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #142)) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #137) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #140) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #143)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #143))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #138))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #141) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #144) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #147)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #147) #("PATH" 0 4 (:parent #151))) #("and R" 0 5 (:parent #147)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #147) #("LIBS" 0 4 (:parent #153))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #147) #("SITE" 0 4 (:parent #154))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #147))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #144) #("On one system:\n" 0 15 (:parent #149))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #144) #("and perhaps a few more.\n" 0 24 (:parent #151))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #142)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #142) #("data" 0 4 (:parent #184))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #142)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #142) #("files" 0 5 (:parent #186))) #("/genotype'" 0 10 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #142) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #145) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #148)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #148) #("data" 0 4 (:parent #152))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #148)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #148) #("settings.py" 0 11 (:parent #154))) #("(see above in\nthis document).\n" 0 30 (:parent #148))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #145) #("You can use the GENENETWORK" 0 27 (:parent #149)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #149) #("FILES" 0 5 (:parent #153))) #("switch to set the datadir, for example\n" 0 39 (:parent #149))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #143))) :mode nil :granularity nil :parent #138) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #143) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #146) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #149))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #144))) :mode nil :granularity nil :parent #138) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #144) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #147) #("This error\n" 0 11 (:parent #150))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #147) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #152))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #147) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #153)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #153) #("LIBS" 0 4 (:parent #157))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #153) #("SITE" 0 4 (:parent #158))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #153))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #145))) :mode nil :granularity nil :parent #138) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #145) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #148) #("The following error\n" 0 20 (:parent #151))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #148) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #153))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #148) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #155))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #148) #("if that works run genenetwork after setting SQL" 0 47 (:parent #157)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #157) #("URI" 0 3 (:parent #161))) #("to something like\n" 0 18 (:parent #157))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #148))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #139) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #142) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #145))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #142) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #146) #("src" 0 3 (:parent #150))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #146))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #142) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #147))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #142) #(" yes\n env GUIX" 0 30 (:parent #148)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #148) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #148))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #142) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #149))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #142) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #150)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #150))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #142) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #151))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #142) #(" which should have the same HASH values " 0 48 (:parent #152)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #152) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #156))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #152)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #152)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #152)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #168))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #152)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #152))))))) #56)) #32)) #0 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #36) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #39) #("Install" 0 7 (:parent #42))) #("\n" 0 1 (:parent #39)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #37) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #40) #("Running GN2" 0 11 (:parent #43))) #("\n" 0 1 (:parent #40)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #38) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #41) #("Run MariaDB server" 0 18 (:parent #44))) #("\n" 0 1 (:parent #41))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #38) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #42) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #45) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #48) #("Install MariaDB with GNU GUIx" 0 29 (:parent #51))) #("\n" 0 1 (:parent #48)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #42) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #46) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #49) #("Load the small database in MySQL" 0 32 (:parent #52))) #("\n" 0 1 (:parent #49)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #39) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #42) #("GN2 Dependency Graph" 0 20 (:parent #45))) #("\n" 0 1 (:parent #42)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #40) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #43) #("Working with the GN2 source code" 0 32 (:parent #46))) #("\n" 0 1 (:parent #43)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #41) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #44) #("Read more" 0 9 (:parent #47))) #("\n" 0 1 (:parent #44)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #42) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #45) #("Trouble shooting" 0 16 (:parent #48))) #("\n" 0 1 (:parent #45))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #42) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #49) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #52) #("ImportError: No module named jinja2" 0 35 (:parent #55))) #("\n" 0 1 (:parent #52)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #50) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #53) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #56)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #56) #("data" 0 4 (:parent #60))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #56)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #56) #("files" 0 5 (:parent #62))) #("/genotype'" 0 10 (:parent #56))) #("\n" 0 1 (:parent #53)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #51) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #54) #("Can't run a module" 0 18 (:parent #57))) #("\n" 0 1 (:parent #54)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #52) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #55) #("Rpy2 error 'show' now found" 0 27 (:parent #58))) #("\n" 0 1 (:parent #55)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #53) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #56) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #59))) #("\n" 0 1 (:parent #56)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #43) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #46) #("IRC session" 0 11 (:parent #49))) #("\n" 0 1 (:parent #46)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #44) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #47) #("NOTES" 0 5 (:parent #50))) #("\n" 0 1 (:parent #47))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #44) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #48) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #51) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #54) #("Deploying GN2 official" 0 22 (:parent #57))) #("\n" 0 1 (:parent #54)))))))) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #0) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #3) #("Introduction" 0 12 (:parent #6))) #("\n" 0 1 (:parent #3)))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #80))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #126) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #129))) #80 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #131))) :mode nil :granularity nil :parent #126) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #131) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #134) #("Large system deployments can get very " 0 38 (:parent #137)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #137) #("complex" 0 7 (:parent #141))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #143))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #138) #("GNU Guix" 0 8 (:parent #144))) #(".\n" 0 2 (:parent #138))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #134) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #139)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #139) #("GN2 Dependency Graph" 0 20 (:parent #143))) #(".\n" 0 2 (:parent #139))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #132))) :mode nil :granularity nil :parent #126) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #132) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #135) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #138)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #138)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #138))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #133) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #136) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #139)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #139) #("default" 0 7 (:parent #143)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #143) #("settings.py" 0 11 (:parent #147)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #139))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #136) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #141))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #136) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #143))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #134))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #137))) :mode section :granularity nil :parent #134) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #137) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #140) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #143) #("Note: we moved to MariaDB" 0 25 (:parent #146))) #("\n" 0 1 (:parent #143))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #140) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #144))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #140) #("As root configure and run\n" 0 26 (:parent #145))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #140) #("If you want to run as root you may have to set\n" 0 47 (:parent #147))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #140) #("You also need to set\n" 0 21 (:parent #149))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #140) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #151))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #140) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #152))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #140) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #154))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #140) #("When you get errors like:\n" 0 26 (:parent #156))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #140)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #140) #("you may need to set\n" 0 20 (:parent #158))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #138))) :mode nil :granularity nil :parent #134) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #138) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #141) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #144)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #144) #("webqtl" 0 6 (:parent #148))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #144) #("s" 0 1 (:parent #149))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #144)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #144) #("webqtl" 0 6 (:parent #151))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #144) #("plant" 0 5 (:parent #152))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #144))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #141) #("Download one database from\n" 0 27 (:parent #145))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #141) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #141) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #141) #("Check the md5sum.\n" 0 18 (:parent #148))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #141) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #149))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #141) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #151))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #141) #("and\n" 0 4 (:parent #153))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #141) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #155))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #141) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #157))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #141) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #158))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #141) #("Note for the plant database you can rename it to db" 0 51 (:parent #159)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #159) #("webqtl" 0 6 (:parent #163))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #159) #("s" 0 1 (:parent #164))) #(", or\nchange the settings in etc/default" 0 39 (:parent #159)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #159) #("settings.py" 0 11 (:parent #166))) #("to match your path.\n" 0 20 (:parent #159)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #135) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #138) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #141))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #138) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #142)) #("\n" 0 1 (:parent #142))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #136))) :mode nil :granularity nil :parent #126) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #136) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #139) #("See " 0 4 (:parent #142)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #142)) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #137) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #140) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #143)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #143))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #138))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #141) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #144) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #147)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #147) #("PATH" 0 4 (:parent #151))) #("and R" 0 5 (:parent #147)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #147) #("LIBS" 0 4 (:parent #153))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #147) #("SITE" 0 4 (:parent #154))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #147))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #144) #("On one system:\n" 0 15 (:parent #149))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #144) #("and perhaps a few more.\n" 0 24 (:parent #151))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #142)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #142) #("data" 0 4 (:parent #184))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #142)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #142) #("files" 0 5 (:parent #186))) #("/genotype'" 0 10 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #142) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #145) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #148)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #148) #("data" 0 4 (:parent #152))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #148)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #148) #("settings.py" 0 11 (:parent #154))) #("(see above in\nthis document).\n" 0 30 (:parent #148))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #145) #("You can use the GENENETWORK" 0 27 (:parent #149)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #149) #("FILES" 0 5 (:parent #153))) #("switch to set the datadir, for example\n" 0 39 (:parent #149))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #143))) :mode nil :granularity nil :parent #138) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #143) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #146) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #149))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #144))) :mode nil :granularity nil :parent #138) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #144) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #147) #("This error\n" 0 11 (:parent #150))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #147) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #152))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #147) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #153)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #153) #("LIBS" 0 4 (:parent #157))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #153) #("SITE" 0 4 (:parent #158))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #153))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #145))) :mode nil :granularity nil :parent #138) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #145) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #148) #("The following error\n" 0 20 (:parent #151))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #148) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #153))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #148) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #155))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #148) #("if that works run genenetwork after setting SQL" 0 47 (:parent #157)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #157) #("URI" 0 3 (:parent #161))) #("to something like\n" 0 18 (:parent #157))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #148))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #139) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #142) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #145))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #142) #("#+begin" 0 7 (:parent #146)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #146) #("src" 0 3 (:parent #150))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #146))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #142) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #147))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #142) #(" yes\n env GUIX" 0 30 (:parent #148)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #148) #("PATH" 0 4 (:parent #153))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #148))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #142) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #149))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #142) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #150)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #150))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #142) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #151))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #142) #(" which should have the same HASH values " 0 48 (:parent #152)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #152) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #156))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #152)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #152)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #152)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #152)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #168))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #152)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #152))))))) #56)) #32)) #0 (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #36) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #39) #("Install" 0 7 (:parent #42))) #("\n" 0 1 (:parent #39)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #37) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #40) #("Running GN2" 0 11 (:parent #43))) #("\n" 0 1 (:parent #40)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #38) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #41) #("Run MariaDB server" 0 18 (:parent #44))) #("\n" 0 1 (:parent #41))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #38) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #42) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #45) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #48) #("Install MariaDB with GNU GUIx" 0 29 (:parent #51))) #("\n" 0 1 (:parent #48)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #42) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #46) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #49) #("Load the small database in MySQL" 0 32 (:parent #52))) #("\n" 0 1 (:parent #49)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #39) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #42) #("GN2 Dependency Graph" 0 20 (:parent #45))) #("\n" 0 1 (:parent #42)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #40) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #43) #("Working with the GN2 source code" 0 32 (:parent #46))) #("\n" 0 1 (:parent #43)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #41) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #44) #("Read more" 0 9 (:parent #47))) #("\n" 0 1 (:parent #44)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #42) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #45) #("Trouble shooting" 0 16 (:parent #48))) #("\n" 0 1 (:parent #45))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #42) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #49) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #52) #("ImportError: No module named jinja2" 0 35 (:parent #55))) #("\n" 0 1 (:parent #52)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #50) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #53) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #56)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #56) #("data" 0 4 (:parent #60))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #56)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #56) #("files" 0 5 (:parent #62))) #("/genotype'" 0 10 (:parent #56))) #("\n" 0 1 (:parent #53)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #51) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #54) #("Can't run a module" 0 18 (:parent #57))) #("\n" 0 1 (:parent #54)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #52) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #55) #("Rpy2 error 'show' now found" 0 27 (:parent #58))) #("\n" 0 1 (:parent #55)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #46) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #53) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #56) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #59))) #("\n" 0 1 (:parent #56)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #43) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #46) #("IRC session" 0 11 (:parent #49))) #("\n" 0 1 (:parent #46)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #32) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #44) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #47) #("NOTES" 0 5 (:parent #50))) #("\n" 0 1 (:parent #47))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #44) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #48) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #51) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #54) #("Deploying GN2 official" 0 22 (:parent #57))) #("\n" 0 1 (:parent #54)))))))) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #0) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #3) #("Introduction" 0 12 (:parent #6))) #("\n" 0 1 (:parent #3))))) mapconcat(#f(compiled-function (element) #) ((item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #81))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #127) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #130))) #81 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #132))) :mode nil :granularity nil :parent #127) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #132) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #135) #("Large system deployments can get very " 0 38 (:parent #138)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #138) #("complex" 0 7 (:parent #142))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #138)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #138) #("Guix-notes" 0 10 (:parent #144))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #138))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #135) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #139) #("Guix bioinformatics" 0 19 (:parent #143))) #("and " 0 4 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #139) #("GNU Guix" 0 8 (:parent #145))) #(".\n" 0 2 (:parent #139))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #135) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #140)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #140) #("GN2 Dependency Graph" 0 20 (:parent #144))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #133))) :mode nil :granularity nil :parent #127) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #133) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #136) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #139)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #139)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #139))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #134))) :mode nil :granularity nil :parent #127) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #134) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #137) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #140)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #140) #("default" 0 7 (:parent #144)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #144) #("settings.py" 0 11 (:parent #148)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #140))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #137) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #142))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #137) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #144))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #135))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #138))) :mode section :granularity nil :parent #135) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #138) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #141) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #144) #("Note: we moved to MariaDB" 0 25 (:parent #147))) #("\n" 0 1 (:parent #144))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #141) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #145))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #141) #("As root configure and run\n" 0 26 (:parent #146))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #141) #("If you want to run as root you may have to set\n" 0 47 (:parent #148))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #141) #("You also need to set\n" 0 21 (:parent #150))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #141) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #152))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #141) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #153))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #141) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #155))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #141) #("When you get errors like:\n" 0 26 (:parent #157))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #141) #("you may need to set\n" 0 20 (:parent #159))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #141)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #139))) :mode nil :granularity nil :parent #135) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #139) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #142) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #145)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #145) #("webqtl" 0 6 (:parent #149))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #145) #("s" 0 1 (:parent #150))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #145)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #145) #("webqtl" 0 6 (:parent #152))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #145) #("plant" 0 5 (:parent #153))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #145))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #142) #("Download one database from\n" 0 27 (:parent #146))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #142) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #142) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #142) #("Check the md5sum.\n" 0 18 (:parent #149))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #142) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #150))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #142) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #152))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #142) #("and\n" 0 4 (:parent #154))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #142)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #142) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #156))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #142)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #142) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #158))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #142) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #159))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #142) #("Note for the plant database you can rename it to db" 0 51 (:parent #160)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #160) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #160) #("s" 0 1 (:parent #165))) #(", or\nchange the settings in etc/default" 0 39 (:parent #160)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #160) #("settings.py" 0 11 (:parent #167))) #("to match your path.\n" 0 20 (:parent #160)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #136))) :mode nil :granularity nil :parent #127) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #136) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #139) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #142))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #139) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #("\n" 0 1 (:parent #143))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #137))) :mode nil :granularity nil :parent #127) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #137) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #140) #("See " 0 4 (:parent #143)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #(".\n" 0 2 (:parent #143))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #138))) :mode nil :granularity nil :parent #127) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #138) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #141) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #144)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #144))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #139))) :mode nil :granularity nil :parent #127) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #142))) :mode section :granularity nil :parent #139) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #142) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #145) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #148)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #148) #("PATH" 0 4 (:parent #152))) #("and R" 0 5 (:parent #148)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #148) #("LIBS" 0 4 (:parent #154))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #148) #("SITE" 0 4 (:parent #155))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #148))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #145)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #145) #("On one system:\n" 0 15 (:parent #150))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #145)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #145) #("and perhaps a few more.\n" 0 24 (:parent #152))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #143)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #143) #("data" 0 4 (:parent #185))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #143)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #143) #("files" 0 5 (:parent #187))) #("/genotype'" 0 10 (:parent #143))) :mode nil :granularity nil :parent #139) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #143) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #146) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #149)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #149) #("data" 0 4 (:parent #153))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #149)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #149) #("settings.py" 0 11 (:parent #155))) #("(see above in\nthis document).\n" 0 30 (:parent #149))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #146) #("You can use the GENENETWORK" 0 27 (:parent #150)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #150) #("FILES" 0 5 (:parent #154))) #("switch to set the datadir, for example\n" 0 39 (:parent #150))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #144))) :mode nil :granularity nil :parent #139) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #144) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #147) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #150))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #145))) :mode nil :granularity nil :parent #139) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #145) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #148) #("This error\n" 0 11 (:parent #151))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #148) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #153))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #148) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #154)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #154) #("LIBS" 0 4 (:parent #158))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #154) #("SITE" 0 4 (:parent #159))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #154))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #146))) :mode nil :granularity nil :parent #139) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #146) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #149) #("The following error\n" 0 20 (:parent #152))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #149) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #154))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #149) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #156))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #149) #("if that works run genenetwork after setting SQL" 0 47 (:parent #158)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #158) #("URI" 0 3 (:parent #162))) #("to something like\n" 0 18 (:parent #158))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #149))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #140))) :mode nil :granularity nil :parent #127) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #140) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #143) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #146))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #143) #("#+begin" 0 7 (:parent #147)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #147) #("src" 0 3 (:parent #151))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #147))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #143) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #148))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #143) #(" yes\n env GUIX" 0 30 (:parent #149)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #149) #("PACKAGE" 0 7 (:parent #153))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #149) #("PATH" 0 4 (:parent #154))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #149))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #143) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #150))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #143) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #151)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #151) #("PACKAGE" 0 7 (:parent #155))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #151) #("PATH" 0 4 (:parent #156))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #151))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #143) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #152))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #143) #(" which should have the same HASH values " 0 48 (:parent #153)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #153) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #157))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #153)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #153)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #163))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #164))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #153)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #153)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #168))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #169))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #153)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #153))))))) #57)) #33)) . #0)) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #1) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #4) #("Introduction" 0 12 (:parent #7))) #("\n" 0 1 (:parent #4)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #82))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #128) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #131))) #82 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #133))) :mode nil :granularity nil :parent #128) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #133) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #136) #("Large system deployments can get very " 0 38 (:parent #139)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #139) #("complex" 0 7 (:parent #143))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #139)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #139) #("Guix-notes" 0 10 (:parent #145))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #139))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #136) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #140) #("Guix bioinformatics" 0 19 (:parent #144))) #("and " 0 4 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #140) #("GNU Guix" 0 8 (:parent #146))) #(".\n" 0 2 (:parent #140))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #136) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #141)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #141) #("GN2 Dependency Graph" 0 20 (:parent #145))) #(".\n" 0 2 (:parent #141))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #134))) :mode nil :granularity nil :parent #128) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #134) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #137) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #140)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #140)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #140))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #135))) :mode nil :granularity nil :parent #128) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #135) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #138) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #141)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #141) #("default" 0 7 (:parent #145)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #145) #("settings.py" 0 11 (:parent #149)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #141))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #138) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #143))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #138) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #145))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #136))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #139))) :mode section :granularity nil :parent #136) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #139) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #142) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #145) #("Note: we moved to MariaDB" 0 25 (:parent #148))) #("\n" 0 1 (:parent #145))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #142) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #146))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #142) #("As root configure and run\n" 0 26 (:parent #147))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #142) #("If you want to run as root you may have to set\n" 0 47 (:parent #149))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #142) #("You also need to set\n" 0 21 (:parent #151))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #142) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #153))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #142) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #154))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #142) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #156))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #142) #("When you get errors like:\n" 0 26 (:parent #158))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #142) #("you may need to set\n" 0 20 (:parent #160))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #140))) :mode nil :granularity nil :parent #136) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #140) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #143) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #146)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #150))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #146) #("s" 0 1 (:parent #151))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #146)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #146) #("plant" 0 5 (:parent #154))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #146))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #143) #("Download one database from\n" 0 27 (:parent #147))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #143) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #143) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #143) #("Check the md5sum.\n" 0 18 (:parent #150))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #143) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #151))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #143) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #153))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #143) #("and\n" 0 4 (:parent #155))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #143) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #157))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #143) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #159))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #143) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #160))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #143) #("Note for the plant database you can rename it to db" 0 51 (:parent #161)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #161) #("webqtl" 0 6 (:parent #165))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #161) #("s" 0 1 (:parent #166))) #(", or\nchange the settings in etc/default" 0 39 (:parent #161)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #161) #("settings.py" 0 11 (:parent #168))) #("to match your path.\n" 0 20 (:parent #161)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #137))) :mode nil :granularity nil :parent #128) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #137) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #140) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #143))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #140) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #("\n" 0 1 (:parent #144))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #138))) :mode nil :granularity nil :parent #128) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #138) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #141) #("See " 0 4 (:parent #144)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #(".\n" 0 2 (:parent #144))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #139))) :mode nil :granularity nil :parent #128) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #139) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #142) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #145)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #145))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #140))) :mode nil :granularity nil :parent #128) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #143))) :mode section :granularity nil :parent #140) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #143) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #146) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #149)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #149) #("PATH" 0 4 (:parent #153))) #("and R" 0 5 (:parent #149)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #149) #("LIBS" 0 4 (:parent #155))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #149) #("SITE" 0 4 (:parent #156))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #149))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #146)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #146) #("On one system:\n" 0 15 (:parent #151))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #146)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #146) #("and perhaps a few more.\n" 0 24 (:parent #153))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #144)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #144) #("data" 0 4 (:parent #186))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #144)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #144) #("files" 0 5 (:parent #188))) #("/genotype'" 0 10 (:parent #144))) :mode nil :granularity nil :parent #140) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #144) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #147) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #150)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #150) #("data" 0 4 (:parent #154))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #150)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #150) #("settings.py" 0 11 (:parent #156))) #("(see above in\nthis document).\n" 0 30 (:parent #150))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #147) #("You can use the GENENETWORK" 0 27 (:parent #151)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #151) #("FILES" 0 5 (:parent #155))) #("switch to set the datadir, for example\n" 0 39 (:parent #151))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #145))) :mode nil :granularity nil :parent #140) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #145) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #148) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #151))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #146))) :mode nil :granularity nil :parent #140) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #146) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #149) #("This error\n" 0 11 (:parent #152))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #149) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #154))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #149) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #155)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #155) #("LIBS" 0 4 (:parent #159))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #155) #("SITE" 0 4 (:parent #160))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #155))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #147))) :mode nil :granularity nil :parent #140) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #147) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #150) #("The following error\n" 0 20 (:parent #153))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #150) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #155))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #150) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #157))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #150) #("if that works run genenetwork after setting SQL" 0 47 (:parent #159)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #159) #("URI" 0 3 (:parent #163))) #("to something like\n" 0 18 (:parent #159))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #150))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #141))) :mode nil :granularity nil :parent #128) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #141) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #144) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #147))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #144) #("#+begin" 0 7 (:parent #148)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #148) #("src" 0 3 (:parent #152))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #148))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #144) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #149))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #144) #(" yes\n env GUIX" 0 30 (:parent #150)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #150) #("PATH" 0 4 (:parent #155))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #150))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #144) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #151))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #144) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #152)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #156))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #157))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #152))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #144) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #153))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #144) #(" which should have the same HASH values " 0 48 (:parent #154)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #154) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #158))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #154)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #154)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #154)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #164))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #165))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #154)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #154)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #169))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #170))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #154)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #154))))))) #58)) #34)) . #0)) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #2) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #5) #("Install" 0 7 (:parent #8))) #("\n" 0 1 (:parent #5)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #83))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #129) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #132))) #83 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #134))) :mode nil :granularity nil :parent #129) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #134) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #137) #("Large system deployments can get very " 0 38 (:parent #140)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #140) #("complex" 0 7 (:parent #144))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #140)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #140) #("Guix-notes" 0 10 (:parent #146))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #140))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #137) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #141) #("Guix bioinformatics" 0 19 (:parent #145))) #("and " 0 4 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #141) #("GNU Guix" 0 8 (:parent #147))) #(".\n" 0 2 (:parent #141))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #137) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #142)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #142) #("GN2 Dependency Graph" 0 20 (:parent #146))) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #135))) :mode nil :granularity nil :parent #129) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #135) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #138) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #141)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #141)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #141))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #136))) :mode nil :granularity nil :parent #129) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #136) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #139) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #142)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #142) #("default" 0 7 (:parent #146)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #146) #("settings.py" 0 11 (:parent #150)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #142))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #139)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #139) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #144))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #139)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #139) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #146))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #137))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #140))) :mode section :granularity nil :parent #137) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #140) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #143) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #146) #("Note: we moved to MariaDB" 0 25 (:parent #149))) #("\n" 0 1 (:parent #146))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #143) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #147))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #143) #("As root configure and run\n" 0 26 (:parent #148))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #143) #("If you want to run as root you may have to set\n" 0 47 (:parent #150))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #143) #("You also need to set\n" 0 21 (:parent #152))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #143) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #154))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #143) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #155))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #143) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #157))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #143) #("When you get errors like:\n" 0 26 (:parent #159))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #143) #("you may need to set\n" 0 20 (:parent #161))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #143)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #141))) :mode nil :granularity nil :parent #137) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #141) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #144) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #147)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #147) #("webqtl" 0 6 (:parent #151))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #147) #("s" 0 1 (:parent #152))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #147)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #147) #("webqtl" 0 6 (:parent #154))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #147) #("plant" 0 5 (:parent #155))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #147))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #144) #("Download one database from\n" 0 27 (:parent #148))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #144) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #144) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #144) #("Check the md5sum.\n" 0 18 (:parent #151))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #144) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #152))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #144) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #154))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #144) #("and\n" 0 4 (:parent #156))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #144) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #158))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #144) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #160))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #144) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #161))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #144) #("Note for the plant database you can rename it to db" 0 51 (:parent #162)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #162) #("s" 0 1 (:parent #167))) #(", or\nchange the settings in etc/default" 0 39 (:parent #162)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #169))) #("to match your path.\n" 0 20 (:parent #162)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #138))) :mode nil :granularity nil :parent #129) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #138) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #141) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #144))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #141) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #139))) :mode nil :granularity nil :parent #129) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #139) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #142) #("See " 0 4 (:parent #145)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #140))) :mode nil :granularity nil :parent #129) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #140) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #143) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #146)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #146))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #141))) :mode nil :granularity nil :parent #129) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #144) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #147) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #150)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #150) #("PATH" 0 4 (:parent #154))) #("and R" 0 5 (:parent #150)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #150) #("LIBS" 0 4 (:parent #156))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #150) #("SITE" 0 4 (:parent #157))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #150))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #147)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #147) #("On one system:\n" 0 15 (:parent #152))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #147)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #147) #("and perhaps a few more.\n" 0 24 (:parent #154))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #145)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #145) #("data" 0 4 (:parent #187))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #145)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #145) #("files" 0 5 (:parent #189))) #("/genotype'" 0 10 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #145) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #148) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #151)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #151) #("data" 0 4 (:parent #155))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #151)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #151) #("settings.py" 0 11 (:parent #157))) #("(see above in\nthis document).\n" 0 30 (:parent #151))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #148) #("You can use the GENENETWORK" 0 27 (:parent #152)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #152) #("FILES" 0 5 (:parent #156))) #("switch to set the datadir, for example\n" 0 39 (:parent #152))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #146))) :mode nil :granularity nil :parent #141) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #146) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #149) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #152))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #147))) :mode nil :granularity nil :parent #141) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #147) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #150) #("This error\n" 0 11 (:parent #153))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #150) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #155))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #150) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #156)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #156) #("SITE" 0 4 (:parent #161))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #156))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #148))) :mode nil :granularity nil :parent #141) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #148) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #151) #("The following error\n" 0 20 (:parent #154))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #151) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #156))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #151) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #158))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #151) #("if that works run genenetwork after setting SQL" 0 47 (:parent #160)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #160) #("URI" 0 3 (:parent #164))) #("to something like\n" 0 18 (:parent #160))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #151))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #142))) :mode nil :granularity nil :parent #129) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #142) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #145) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #148))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #145) #("#+begin" 0 7 (:parent #149)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #149) #("src" 0 3 (:parent #153))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #149))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #145) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #150))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #145) #(" yes\n env GUIX" 0 30 (:parent #151)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #151) #("PACKAGE" 0 7 (:parent #155))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #151) #("PATH" 0 4 (:parent #156))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #151))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #145) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #152))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #145) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #153)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #157))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #158))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #153))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #145) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #154))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #145) #(" which should have the same HASH values " 0 48 (:parent #155)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #155) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #159))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #155)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #155)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #155)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #165))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #166))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #155)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #155)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #155)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #173))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #174))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #155))))))) #59)) #35)) . #0)) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #3) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #6) #("Running GN2" 0 11 (:parent #9))) #("\n" 0 1 (:parent #6)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #84))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #130) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #133))) #84 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #135))) :mode nil :granularity nil :parent #130) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #135) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #138) #("Large system deployments can get very " 0 38 (:parent #141)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #141) #("complex" 0 7 (:parent #145))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #141) #("Guix-notes" 0 10 (:parent #147))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #141))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #138) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #142) #("Guix bioinformatics" 0 19 (:parent #146))) #("and " 0 4 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #142) #("GNU Guix" 0 8 (:parent #148))) #(".\n" 0 2 (:parent #142))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #138) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #143)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #143) #("GN2 Dependency Graph" 0 20 (:parent #147))) #(".\n" 0 2 (:parent #143))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #136))) :mode nil :granularity nil :parent #130) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #136) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #139) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #142)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #142)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #142))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #137))) :mode nil :granularity nil :parent #130) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #137) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #140) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #143)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #143) #("default" 0 7 (:parent #147)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #147) #("settings.py" 0 11 (:parent #151)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #143))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #140)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #140) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #145))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #140)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #140) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #147))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #138))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #141) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #144) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #147) #("Note: we moved to MariaDB" 0 25 (:parent #150))) #("\n" 0 1 (:parent #147))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #144) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #148))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #144) #("As root configure and run\n" 0 26 (:parent #149))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #144) #("If you want to run as root you may have to set\n" 0 47 (:parent #151))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #144) #("You also need to set\n" 0 21 (:parent #153))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #144) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #155))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #144) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #156))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #144) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #158))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #144) #("When you get errors like:\n" 0 26 (:parent #160))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #144) #("you may need to set\n" 0 20 (:parent #162))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #142) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #145) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #148)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #152))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #148) #("s" 0 1 (:parent #153))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #148)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #148) #("plant" 0 5 (:parent #156))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #148))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #145) #("Download one database from\n" 0 27 (:parent #149))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #145) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #145) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #145) #("Check the md5sum.\n" 0 18 (:parent #152))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #145) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #153))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #145) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #155))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #145) #("and\n" 0 4 (:parent #157))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #145) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #159))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #145) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #161))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #145) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #162))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #145) #("Note for the plant database you can rename it to db" 0 51 (:parent #163)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #163) #("webqtl" 0 6 (:parent #167))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #163) #("s" 0 1 (:parent #168))) #(", or\nchange the settings in etc/default" 0 39 (:parent #163)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #163) #("settings.py" 0 11 (:parent #170))) #("to match your path.\n" 0 20 (:parent #163)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #139))) :mode nil :granularity nil :parent #130) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #139) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #142) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #145))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #142) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #140))) :mode nil :granularity nil :parent #130) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #140) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #143) #("See " 0 4 (:parent #146)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #141))) :mode nil :granularity nil :parent #130) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #141) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #144) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #147)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #147))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #142))) :mode nil :granularity nil :parent #130) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #145) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #148) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #151)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #151) #("PATH" 0 4 (:parent #155))) #("and R" 0 5 (:parent #151)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #151) #("LIBS" 0 4 (:parent #157))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #151) #("SITE" 0 4 (:parent #158))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #151))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #148)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #148) #("On one system:\n" 0 15 (:parent #153))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #148)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #148) #("and perhaps a few more.\n" 0 24 (:parent #155))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #146)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #146) #("data" 0 4 (:parent #188))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #146)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #146) #("files" 0 5 (:parent #190))) #("/genotype'" 0 10 (:parent #146))) :mode nil :granularity nil :parent #142) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #146) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #149) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #152)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #152) #("data" 0 4 (:parent #156))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #152)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #152) #("settings.py" 0 11 (:parent #158))) #("(see above in\nthis document).\n" 0 30 (:parent #152))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #149) #("You can use the GENENETWORK" 0 27 (:parent #153)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #153) #("FILES" 0 5 (:parent #157))) #("switch to set the datadir, for example\n" 0 39 (:parent #153))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #147))) :mode nil :granularity nil :parent #142) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #147) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #150) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #153))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #148))) :mode nil :granularity nil :parent #142) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #148) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #151) #("This error\n" 0 11 (:parent #154))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #151) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #156))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #151) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #157)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #157) #("LIBS" 0 4 (:parent #161))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #157) #("SITE" 0 4 (:parent #162))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #157))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #149))) :mode nil :granularity nil :parent #142) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #149) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #152) #("The following error\n" 0 20 (:parent #155))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #152) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #157))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #152) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #159))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #152) #("if that works run genenetwork after setting SQL" 0 47 (:parent #161)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #161) #("URI" 0 3 (:parent #165))) #("to something like\n" 0 18 (:parent #161))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #152))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #143))) :mode nil :granularity nil :parent #130) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #143) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #146) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #149))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #146) #("#+begin" 0 7 (:parent #150)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #150) #("src" 0 3 (:parent #154))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #150))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #146) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #151))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #146) #(" yes\n env GUIX" 0 30 (:parent #152)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #156))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #152) #("PATH" 0 4 (:parent #157))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #152))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #146) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #153))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #146) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #154)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #158))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #159))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #154))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #146) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #155))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #146) #(" which should have the same HASH values " 0 48 (:parent #156)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #156) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #160))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #156)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #156)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #156)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #166))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #167))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #156)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #156)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #156)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #156))))))) #60)) #36)) . #0)) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #7) #("Run MariaDB server" 0 18 (:parent #10))) #("\n" 0 1 (:parent #7))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #4) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #14) #("Install MariaDB with GNU GUIx" 0 29 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #15) #("Load the small database in MySQL" 0 32 (:parent #18))) #("\n" 0 1 (:parent #15)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #85))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #131) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #134))) #85 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #136))) :mode nil :granularity nil :parent #131) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #136) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #139) #("Large system deployments can get very " 0 38 (:parent #142)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #142) #("complex" 0 7 (:parent #146))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #142)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #142) #("Guix-notes" 0 10 (:parent #148))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #142))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #139) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #143) #("Guix bioinformatics" 0 19 (:parent #147))) #("and " 0 4 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #143) #("GNU Guix" 0 8 (:parent #149))) #(".\n" 0 2 (:parent #143))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #139) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #144)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #144) #("GN2 Dependency Graph" 0 20 (:parent #148))) #(".\n" 0 2 (:parent #144))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #137))) :mode nil :granularity nil :parent #131) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #137) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #140) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #143)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #143)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #143))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #138))) :mode nil :granularity nil :parent #131) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #138) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #141) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #144)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #144) #("default" 0 7 (:parent #148)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #148) #("settings.py" 0 11 (:parent #152)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #144))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #141)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #141) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #146))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #141)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #141) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #148))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #139))) :mode nil :granularity nil :parent #131) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #142))) :mode section :granularity nil :parent #139) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #142) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #145) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #148) #("Note: we moved to MariaDB" 0 25 (:parent #151))) #("\n" 0 1 (:parent #148))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #145) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #149))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #145) #("As root configure and run\n" 0 26 (:parent #150))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #145) #("If you want to run as root you may have to set\n" 0 47 (:parent #152))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #145) #("You also need to set\n" 0 21 (:parent #154))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #145) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #156))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #145) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #157))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #145) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #159))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #145) #("When you get errors like:\n" 0 26 (:parent #161))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #145) #("you may need to set\n" 0 20 (:parent #163))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #143))) :mode nil :granularity nil :parent #139) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #143) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #146) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #149)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #149) #("s" 0 1 (:parent #154))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #149)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #149) #("plant" 0 5 (:parent #157))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #149))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #146) #("Download one database from\n" 0 27 (:parent #150))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #146) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #146) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #146) #("Check the md5sum.\n" 0 18 (:parent #153))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #146) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #154))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #146) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #156))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #146) #("and\n" 0 4 (:parent #158))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #146) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #160))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #146) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #162))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #146) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #163))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #146) #("Note for the plant database you can rename it to db" 0 51 (:parent #164)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #164) #("s" 0 1 (:parent #169))) #(", or\nchange the settings in etc/default" 0 39 (:parent #164)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #164) #("settings.py" 0 11 (:parent #171))) #("to match your path.\n" 0 20 (:parent #164)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #140))) :mode nil :granularity nil :parent #131) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #140) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #143) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #146))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #143) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #141))) :mode nil :granularity nil :parent #131) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #141) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #144) #("See " 0 4 (:parent #147)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #142))) :mode nil :granularity nil :parent #131) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #142) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #145) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #148)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #148))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #143))) :mode nil :granularity nil :parent #131) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #146) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #149) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #152)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #152) #("PATH" 0 4 (:parent #156))) #("and R" 0 5 (:parent #152)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #152) #("LIBS" 0 4 (:parent #158))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #152) #("SITE" 0 4 (:parent #159))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #152))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #149)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #149) #("On one system:\n" 0 15 (:parent #154))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #149)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #149) #("and perhaps a few more.\n" 0 24 (:parent #156))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #147)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #147) #("data" 0 4 (:parent #189))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #147)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #147) #("files" 0 5 (:parent #191))) #("/genotype'" 0 10 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #147) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #150) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #153)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #153) #("data" 0 4 (:parent #157))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #153)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #153) #("settings.py" 0 11 (:parent #159))) #("(see above in\nthis document).\n" 0 30 (:parent #153))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #150) #("You can use the GENENETWORK" 0 27 (:parent #154)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #154) #("FILES" 0 5 (:parent #158))) #("switch to set the datadir, for example\n" 0 39 (:parent #154))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #148))) :mode nil :granularity nil :parent #143) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #148) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #151) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #154))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #149))) :mode nil :granularity nil :parent #143) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #149) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #152) #("This error\n" 0 11 (:parent #155))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #152) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #157))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #152) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #158)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #158) #("SITE" 0 4 (:parent #163))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #158))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #150))) :mode nil :granularity nil :parent #143) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #150) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #153) #("The following error\n" 0 20 (:parent #156))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #153) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #158))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #153) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #160))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #153) #("if that works run genenetwork after setting SQL" 0 47 (:parent #162)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #162) #("URI" 0 3 (:parent #166))) #("to something like\n" 0 18 (:parent #162))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #153))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #144))) :mode nil :granularity nil :parent #131) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #144) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #147) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #150))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #147) #("#+begin" 0 7 (:parent #151)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #151) #("src" 0 3 (:parent #155))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #151))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #147) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #152))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #147) #(" yes\n env GUIX" 0 30 (:parent #153)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #157))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #153) #("PATH" 0 4 (:parent #158))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #153))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #147) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #154))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #147) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #155)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #159))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #160))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #155))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #147) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #156))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #147) #(" which should have the same HASH values " 0 48 (:parent #157)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #157) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #161))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #157)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #157)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #157)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #157) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #157) #("PATH" 0 4 (:parent #168))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #157)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #157)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #157) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #157) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #157)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #157) #("PACKAGE" 0 7 (:parent #175))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #157) #("PATH" 0 4 (:parent #176))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #157)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #157))))))) #61)) #37)) . #0)) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #5) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #8) #("GN2 Dependency Graph" 0 20 (:parent #11))) #("\n" 0 1 (:parent #8)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #86))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #132) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #135))) #86 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #137))) :mode nil :granularity nil :parent #132) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #137) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #140) #("Large system deployments can get very " 0 38 (:parent #143)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #143) #("complex" 0 7 (:parent #147))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #143)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #143) #("Guix-notes" 0 10 (:parent #149))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #143))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #140) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #144) #("Guix bioinformatics" 0 19 (:parent #148))) #("and " 0 4 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #144) #("GNU Guix" 0 8 (:parent #150))) #(".\n" 0 2 (:parent #144))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #140) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #145)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #145) #("GN2 Dependency Graph" 0 20 (:parent #149))) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #138))) :mode nil :granularity nil :parent #132) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #138) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #141) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #144)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #144)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #144))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #139))) :mode nil :granularity nil :parent #132) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #139) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #142) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #145)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #145) #("default" 0 7 (:parent #149)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #149) #("settings.py" 0 11 (:parent #153)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #145))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #142)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #142) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #147))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #142)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #142) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #149))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #140))) :mode nil :granularity nil :parent #132) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #143))) :mode section :granularity nil :parent #140) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #143) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #146) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #149) #("Note: we moved to MariaDB" 0 25 (:parent #152))) #("\n" 0 1 (:parent #149))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #146) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #150))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #146) #("As root configure and run\n" 0 26 (:parent #151))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #146) #("If you want to run as root you may have to set\n" 0 47 (:parent #153))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #146) #("You also need to set\n" 0 21 (:parent #155))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #146) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #157))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #146) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #158))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #146) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #160))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #146) #("When you get errors like:\n" 0 26 (:parent #162))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #146) #("you may need to set\n" 0 20 (:parent #164))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #144))) :mode nil :granularity nil :parent #140) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #144) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #147) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #150)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #154))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #150) #("s" 0 1 (:parent #155))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #150)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #150) #("plant" 0 5 (:parent #158))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #150))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #147) #("Download one database from\n" 0 27 (:parent #151))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #147) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #147) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #147) #("Check the md5sum.\n" 0 18 (:parent #154))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #147) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #155))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #147) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #157))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #147) #("and\n" 0 4 (:parent #159))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #147) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #161))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #147) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #163))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #147) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #164))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #147) #("Note for the plant database you can rename it to db" 0 51 (:parent #165)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #165) #("webqtl" 0 6 (:parent #169))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #165) #("s" 0 1 (:parent #170))) #(", or\nchange the settings in etc/default" 0 39 (:parent #165)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #165) #("settings.py" 0 11 (:parent #172))) #("to match your path.\n" 0 20 (:parent #165)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #141))) :mode nil :granularity nil :parent #132) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #141) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #144) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #147))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #144) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #142))) :mode nil :granularity nil :parent #132) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #142) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #145) #("See " 0 4 (:parent #148)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #143))) :mode nil :granularity nil :parent #132) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #143) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #146) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #149)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #149))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #144))) :mode nil :granularity nil :parent #132) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #147) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #150) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #153)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #153) #("PATH" 0 4 (:parent #157))) #("and R" 0 5 (:parent #153)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #153) #("LIBS" 0 4 (:parent #159))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #153) #("SITE" 0 4 (:parent #160))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #153))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #150)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #150) #("On one system:\n" 0 15 (:parent #155))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #150)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #150) #("and perhaps a few more.\n" 0 24 (:parent #157))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #148)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #148) #("data" 0 4 (:parent #190))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #148)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #148) #("files" 0 5 (:parent #192))) #("/genotype'" 0 10 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #148) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #151) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #154)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #154) #("data" 0 4 (:parent #158))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #154)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #154) #("settings.py" 0 11 (:parent #160))) #("(see above in\nthis document).\n" 0 30 (:parent #154))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #151) #("You can use the GENENETWORK" 0 27 (:parent #155)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #155) #("FILES" 0 5 (:parent #159))) #("switch to set the datadir, for example\n" 0 39 (:parent #155))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #149))) :mode nil :granularity nil :parent #144) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #149) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #152) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #155))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #150))) :mode nil :granularity nil :parent #144) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #150) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #153) #("This error\n" 0 11 (:parent #156))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #153) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #158))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #153) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #159)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #159) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #159) #("SITE" 0 4 (:parent #164))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #159))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #151))) :mode nil :granularity nil :parent #144) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #151) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #154) #("The following error\n" 0 20 (:parent #157))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #154) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #159))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #154) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #161))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #154) #("if that works run genenetwork after setting SQL" 0 47 (:parent #163)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #163) #("URI" 0 3 (:parent #167))) #("to something like\n" 0 18 (:parent #163))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #154))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #145))) :mode nil :granularity nil :parent #132) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #145) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #148) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #151))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #148) #("#+begin" 0 7 (:parent #152)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #152) #("src" 0 3 (:parent #156))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #152))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #148) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #153))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #148) #(" yes\n env GUIX" 0 30 (:parent #154)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #158))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #154) #("PATH" 0 4 (:parent #159))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #154))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #148) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #155))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #148) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #156)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #160))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #161))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #156))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #148) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #157))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #148) #(" which should have the same HASH values " 0 48 (:parent #158)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #158) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #162))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #158)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #158)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #158) #("PACKAGE" 0 7 (:parent #168))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #158) #("PATH" 0 4 (:parent #169))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #158)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #158)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #158) #("PACKAGE" 0 7 (:parent #173))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #158) #("PATH" 0 4 (:parent #174))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #158)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #158) #("PACKAGE" 0 7 (:parent #176))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #158) #("PATH" 0 4 (:parent #177))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #158)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #158))))))) #62)) #38)) . #0)) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #9) #("Working with the GN2 source code" 0 32 (:parent #12))) #("\n" 0 1 (:parent #9)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #87))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #133) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #136))) #87 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #138))) :mode nil :granularity nil :parent #133) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #138) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #141) #("Large system deployments can get very " 0 38 (:parent #144)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #144) #("complex" 0 7 (:parent #148))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #144)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #144) #("Guix-notes" 0 10 (:parent #150))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #144))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #141) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #145) #("Guix bioinformatics" 0 19 (:parent #149))) #("and " 0 4 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #145) #("GNU Guix" 0 8 (:parent #151))) #(".\n" 0 2 (:parent #145))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #141) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #146)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #146) #("GN2 Dependency Graph" 0 20 (:parent #150))) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #139))) :mode nil :granularity nil :parent #133) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #139) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #142) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #145)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #145)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #145))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #140))) :mode nil :granularity nil :parent #133) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #140) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #143) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #146)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #146) #("default" 0 7 (:parent #150)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #150) #("settings.py" 0 11 (:parent #154)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #146))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #143)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #143) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #148))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #143)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #143) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #150))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #141))) :mode nil :granularity nil :parent #133) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #144) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #147) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #150) #("Note: we moved to MariaDB" 0 25 (:parent #153))) #("\n" 0 1 (:parent #150))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #147) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #151))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #147) #("As root configure and run\n" 0 26 (:parent #152))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #147) #("If you want to run as root you may have to set\n" 0 47 (:parent #154))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #147) #("You also need to set\n" 0 21 (:parent #156))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #147) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #158))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #147) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #159))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #147) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #161))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #147) #("When you get errors like:\n" 0 26 (:parent #163))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #147) #("you may need to set\n" 0 20 (:parent #165))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #145) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #148) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #151)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #151) #("s" 0 1 (:parent #156))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #151)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #151) #("plant" 0 5 (:parent #159))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #151))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #148) #("Download one database from\n" 0 27 (:parent #152))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #148) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #148) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #148) #("Check the md5sum.\n" 0 18 (:parent #155))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #148) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #156))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #148) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #158))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #148) #("and\n" 0 4 (:parent #160))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #148) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #162))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #148) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #164))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #148) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #165))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #148) #("Note for the plant database you can rename it to db" 0 51 (:parent #166)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #170))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #166) #("s" 0 1 (:parent #171))) #(", or\nchange the settings in etc/default" 0 39 (:parent #166)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #166) #("settings.py" 0 11 (:parent #173))) #("to match your path.\n" 0 20 (:parent #166)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #142))) :mode nil :granularity nil :parent #133) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #142) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #145) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #148))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #145) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #143))) :mode nil :granularity nil :parent #133) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #143) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #146) #("See " 0 4 (:parent #149)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #144))) :mode nil :granularity nil :parent #133) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #144) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #147) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #150)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #150))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #145))) :mode nil :granularity nil :parent #133) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #148) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #151) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #154)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #154) #("PATH" 0 4 (:parent #158))) #("and R" 0 5 (:parent #154)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #154) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #154) #("SITE" 0 4 (:parent #161))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #154))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #151)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #151) #("On one system:\n" 0 15 (:parent #156))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #151)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #151) #("and perhaps a few more.\n" 0 24 (:parent #158))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #149)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #149) #("data" 0 4 (:parent #191))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #149)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #149) #("files" 0 5 (:parent #193))) #("/genotype'" 0 10 (:parent #149))) :mode nil :granularity nil :parent #145) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #149) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #152) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #155)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #155) #("data" 0 4 (:parent #159))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #155)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #155) #("settings.py" 0 11 (:parent #161))) #("(see above in\nthis document).\n" 0 30 (:parent #155))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #152) #("You can use the GENENETWORK" 0 27 (:parent #156)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #156) #("FILES" 0 5 (:parent #160))) #("switch to set the datadir, for example\n" 0 39 (:parent #156))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #150))) :mode nil :granularity nil :parent #145) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #150) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #153) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #156))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #151))) :mode nil :granularity nil :parent #145) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #151) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #154) #("This error\n" 0 11 (:parent #157))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #154) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #159))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #154) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #160)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #160) #("LIBS" 0 4 (:parent #164))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #160) #("SITE" 0 4 (:parent #165))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #160))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #152))) :mode nil :granularity nil :parent #145) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #152) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #155) #("The following error\n" 0 20 (:parent #158))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #155) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #160))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #155) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #162))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #155) #("if that works run genenetwork after setting SQL" 0 47 (:parent #164)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #164) #("URI" 0 3 (:parent #168))) #("to something like\n" 0 18 (:parent #164))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #155))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #146))) :mode nil :granularity nil :parent #133) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #146) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #149) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #152))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #149) #("#+begin" 0 7 (:parent #153)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #153) #("src" 0 3 (:parent #157))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #153))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #149) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #154))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #149) #(" yes\n env GUIX" 0 30 (:parent #155)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #155) #("PACKAGE" 0 7 (:parent #159))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #155) #("PATH" 0 4 (:parent #160))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #155))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #149) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #156))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #149) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #157)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #157) #("PACKAGE" 0 7 (:parent #161))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #157) #("PATH" 0 4 (:parent #162))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #157))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #149) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #158))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #149) #(" which should have the same HASH values " 0 48 (:parent #159)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #159) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #163))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #159)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #159)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #159)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #159) #("PACKAGE" 0 7 (:parent #169))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #159) #("PATH" 0 4 (:parent #170))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #159)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #159)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #159) #("PACKAGE" 0 7 (:parent #174))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #159) #("PATH" 0 4 (:parent #175))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #159)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #159) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #159) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #159)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #159))))))) #63)) #39)) . #0)) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #10) #("Read more" 0 9 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #88))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #134) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #137))) #88 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #139))) :mode nil :granularity nil :parent #134) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #139) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #142) #("Large system deployments can get very " 0 38 (:parent #145)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #145) #("complex" 0 7 (:parent #149))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #145)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #145) #("Guix-notes" 0 10 (:parent #151))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #145))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #142) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #146) #("Guix bioinformatics" 0 19 (:parent #150))) #("and " 0 4 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #146) #("GNU Guix" 0 8 (:parent #152))) #(".\n" 0 2 (:parent #146))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #142) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #147)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #147) #("GN2 Dependency Graph" 0 20 (:parent #151))) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #140))) :mode nil :granularity nil :parent #134) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #140) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #143) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #146)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #146)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #146))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #141))) :mode nil :granularity nil :parent #134) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #141) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #144) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #147)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #147) #("default" 0 7 (:parent #151)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #151) #("settings.py" 0 11 (:parent #155)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #147))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #144)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #144) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #149))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #144)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #144) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #151))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #142))) :mode nil :granularity nil :parent #134) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #145) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #148) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #151) #("Note: we moved to MariaDB" 0 25 (:parent #154))) #("\n" 0 1 (:parent #151))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #148) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #152))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #148) #("As root configure and run\n" 0 26 (:parent #153))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #148) #("If you want to run as root you may have to set\n" 0 47 (:parent #155))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #148) #("You also need to set\n" 0 21 (:parent #157))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #148) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #159))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #148) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #160))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #148) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #162))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #148) #("When you get errors like:\n" 0 26 (:parent #164))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #148) #("you may need to set\n" 0 20 (:parent #166))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #146))) :mode nil :granularity nil :parent #142) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #146) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #149) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #152)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #152) #("s" 0 1 (:parent #157))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #152)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #159))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #152) #("plant" 0 5 (:parent #160))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #152))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #149) #("Download one database from\n" 0 27 (:parent #153))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #149) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #149) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #149) #("Check the md5sum.\n" 0 18 (:parent #156))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #149) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #157))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #149) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #159))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #149) #("and\n" 0 4 (:parent #161))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #149) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #163))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #149) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #165))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #149) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #166))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #149) #("Note for the plant database you can rename it to db" 0 51 (:parent #167)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #167) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #167) #("s" 0 1 (:parent #172))) #(", or\nchange the settings in etc/default" 0 39 (:parent #167)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #167) #("settings.py" 0 11 (:parent #174))) #("to match your path.\n" 0 20 (:parent #167)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #143))) :mode nil :granularity nil :parent #134) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #143) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #146) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #149))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #146) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #144))) :mode nil :granularity nil :parent #134) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #144) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #147) #("See " 0 4 (:parent #150)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #145))) :mode nil :granularity nil :parent #134) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #145) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #148) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #151)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #151))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #146))) :mode nil :granularity nil :parent #134) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #149) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #152) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #155)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #155) #("PATH" 0 4 (:parent #159))) #("and R" 0 5 (:parent #155)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #155) #("LIBS" 0 4 (:parent #161))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #155) #("SITE" 0 4 (:parent #162))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #155))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #152)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #152) #("On one system:\n" 0 15 (:parent #157))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #152)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #152) #("and perhaps a few more.\n" 0 24 (:parent #159))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #150)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #150) #("data" 0 4 (:parent #192))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #150)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #150) #("files" 0 5 (:parent #194))) #("/genotype'" 0 10 (:parent #150))) :mode nil :granularity nil :parent #146) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #150) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #153) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #156)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #156) #("data" 0 4 (:parent #160))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #156)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #156) #("settings.py" 0 11 (:parent #162))) #("(see above in\nthis document).\n" 0 30 (:parent #156))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #153) #("You can use the GENENETWORK" 0 27 (:parent #157)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #157) #("FILES" 0 5 (:parent #161))) #("switch to set the datadir, for example\n" 0 39 (:parent #157))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #151) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #154) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #157))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #152) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #155) #("This error\n" 0 11 (:parent #158))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #155) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #160))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #155) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #161)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #161) #("LIBS" 0 4 (:parent #165))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #161) #("SITE" 0 4 (:parent #166))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #161))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #153) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #156) #("The following error\n" 0 20 (:parent #159))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #156) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #161))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #156) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #163))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #156) #("if that works run genenetwork after setting SQL" 0 47 (:parent #165)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #165) #("URI" 0 3 (:parent #169))) #("to something like\n" 0 18 (:parent #165))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #156))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #147))) :mode nil :granularity nil :parent #134) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #147) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #150) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #153))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #150) #("#+begin" 0 7 (:parent #154)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #154) #("src" 0 3 (:parent #158))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #154))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #150) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #155))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #150) #(" yes\n env GUIX" 0 30 (:parent #156)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #156) #("PACKAGE" 0 7 (:parent #160))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #156) #("PATH" 0 4 (:parent #161))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #156))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #150) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #157))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #150) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #158)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #158) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #158) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #158))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #150) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #159))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #150) #(" which should have the same HASH values " 0 48 (:parent #160)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #160) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #164))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #160)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #160)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #160)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #160)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #170))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #160) #("PATH" 0 4 (:parent #171))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #160)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #160)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #175))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #160) #("PATH" 0 4 (:parent #176))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #160)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #178))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #160) #("PATH" 0 4 (:parent #179))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #160)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #160))))))) #64)) #40)) . #0)) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #11) #("Trouble shooting" 0 16 (:parent #14))) #("\n" 0 1 (:parent #11))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #8) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #12) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #18) #("ImportError: No module named jinja2" 0 35 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #12) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #19) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #22)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #22) #("data" 0 4 (:parent #26))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #22)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #22) #("files" 0 5 (:parent #28))) #("/genotype'" 0 10 (:parent #22))) #("\n" 0 1 (:parent #19)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #12) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #20) #("Can't run a module" 0 18 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #12) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #21) #("Rpy2 error 'show' now found" 0 27 (:parent #24))) #("\n" 0 1 (:parent #21)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #12) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #22) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #25))) #("\n" 0 1 (:parent #22)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #89))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #135) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #138))) #89 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #140))) :mode nil :granularity nil :parent #135) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #140) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #143) #("Large system deployments can get very " 0 38 (:parent #146)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #146) #("complex" 0 7 (:parent #150))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #146)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #146) #("Guix-notes" 0 10 (:parent #152))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #146))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #143) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #147)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #147) #("Guix bioinformatics" 0 19 (:parent #151))) #("and " 0 4 (:parent #147)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #147) #("GNU Guix" 0 8 (:parent #153))) #(".\n" 0 2 (:parent #147))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #143) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #148)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #148) #("GN2 Dependency Graph" 0 20 (:parent #152))) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #141))) :mode nil :granularity nil :parent #135) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #141) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #144) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #147)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #147)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #147))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #142))) :mode nil :granularity nil :parent #135) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #142) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #145) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #148)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #148) #("default" 0 7 (:parent #152)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #152) #("settings.py" 0 11 (:parent #156)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #148))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #145)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #145) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #150))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #145)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #145) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #152))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #143))) :mode nil :granularity nil :parent #135) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #146) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #149) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #152) #("Note: we moved to MariaDB" 0 25 (:parent #155))) #("\n" 0 1 (:parent #152))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #149) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #153))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #149) #("As root configure and run\n" 0 26 (:parent #154))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #149) #("If you want to run as root you may have to set\n" 0 47 (:parent #156))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #149) #("You also need to set\n" 0 21 (:parent #158))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #149) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #160))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #149) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #161))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #149) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #163))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #149) #("When you get errors like:\n" 0 26 (:parent #165))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #149) #("you may need to set\n" 0 20 (:parent #167))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #147) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #150) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #153)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #153) #("s" 0 1 (:parent #158))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #153)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #160))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #153) #("plant" 0 5 (:parent #161))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #153))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #150) #("Download one database from\n" 0 27 (:parent #154))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #150) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #150) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #150) #("Check the md5sum.\n" 0 18 (:parent #157))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #150) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #158))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #150) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #160))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #150) #("and\n" 0 4 (:parent #162))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #150) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #164))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #150) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #166))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #150) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #167))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #150) #("Note for the plant database you can rename it to db" 0 51 (:parent #168)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #168) #("s" 0 1 (:parent #173))) #(", or\nchange the settings in etc/default" 0 39 (:parent #168)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #168) #("settings.py" 0 11 (:parent #175))) #("to match your path.\n" 0 20 (:parent #168)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #144))) :mode nil :granularity nil :parent #135) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #144) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #147) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #150))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #147) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #145))) :mode nil :granularity nil :parent #135) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #145) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #148) #("See " 0 4 (:parent #151)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(".\n" 0 2 (:parent #151))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #146))) :mode nil :granularity nil :parent #135) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #146) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #149) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #152)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #152))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #147))) :mode nil :granularity nil :parent #135) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #150) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #153) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #156)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #156) #("PATH" 0 4 (:parent #160))) #("and R" 0 5 (:parent #156)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #156) #("SITE" 0 4 (:parent #163))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #156))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #153)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #153) #("On one system:\n" 0 15 (:parent #158))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #153)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #153) #("and perhaps a few more.\n" 0 24 (:parent #160))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #151)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #151) #("data" 0 4 (:parent #193))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #151)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #151) #("files" 0 5 (:parent #195))) #("/genotype'" 0 10 (:parent #151))) :mode nil :granularity nil :parent #147) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #151) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #154) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #157)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #157) #("data" 0 4 (:parent #161))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #157)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #157) #("settings.py" 0 11 (:parent #163))) #("(see above in\nthis document).\n" 0 30 (:parent #157))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #154) #("You can use the GENENETWORK" 0 27 (:parent #158)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #158) #("FILES" 0 5 (:parent #162))) #("switch to set the datadir, for example\n" 0 39 (:parent #158))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #152) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #155) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #158))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #153) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #156) #("This error\n" 0 11 (:parent #159))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #156) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #161))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #156) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #162)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #162) #("LIBS" 0 4 (:parent #166))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #162) #("SITE" 0 4 (:parent #167))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #162))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #154) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #157) #("The following error\n" 0 20 (:parent #160))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #157) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #162))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #157) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #164))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #157) #("if that works run genenetwork after setting SQL" 0 47 (:parent #166)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #166) #("URI" 0 3 (:parent #170))) #("to something like\n" 0 18 (:parent #166))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #157))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #148))) :mode nil :granularity nil :parent #135) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #148) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #151) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #154))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #151) #("#+begin" 0 7 (:parent #155)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #155) #("src" 0 3 (:parent #159))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #155))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #151) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #156))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #151) #(" yes\n env GUIX" 0 30 (:parent #157)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #157) #("PACKAGE" 0 7 (:parent #161))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #157) #("PATH" 0 4 (:parent #162))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #157))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #151) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #158))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #151) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #159)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #159) #("PACKAGE" 0 7 (:parent #163))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #159) #("PATH" 0 4 (:parent #164))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #159))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #151) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #160))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #151) #(" which should have the same HASH values " 0 48 (:parent #161)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #161) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #165))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #161)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #161)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #161)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #161)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #161) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #161) #("PATH" 0 4 (:parent #172))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #161)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #161)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #161) #("PACKAGE" 0 7 (:parent #176))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #161) #("PATH" 0 4 (:parent #177))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #161)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #161) #("PACKAGE" 0 7 (:parent #179))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #161) #("PATH" 0 4 (:parent #180))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #161)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #161))))))) #65)) #41)) . #0)) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #12) #("IRC session" 0 11 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #90))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #136) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #139))) #90 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #141))) :mode nil :granularity nil :parent #136) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #141) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #144) #("Large system deployments can get very " 0 38 (:parent #147)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #147) #("complex" 0 7 (:parent #151))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #147)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #147) #("Guix-notes" 0 10 (:parent #153))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #147))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #144) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #148) #("Guix bioinformatics" 0 19 (:parent #152))) #("and " 0 4 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #148) #("GNU Guix" 0 8 (:parent #154))) #(".\n" 0 2 (:parent #148))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #144) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #149)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #149) #("GN2 Dependency Graph" 0 20 (:parent #153))) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #142))) :mode nil :granularity nil :parent #136) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #142) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #145) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #148)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #148))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #143))) :mode nil :granularity nil :parent #136) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #143) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #146) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #149)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #149) #("default" 0 7 (:parent #153)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #153) #("settings.py" 0 11 (:parent #157)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #149))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #146)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #146) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #151))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #146)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #146) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #153))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #144))) :mode nil :granularity nil :parent #136) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #147) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #150) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #153) #("Note: we moved to MariaDB" 0 25 (:parent #156))) #("\n" 0 1 (:parent #153))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #150) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #154))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #150) #("As root configure and run\n" 0 26 (:parent #155))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #150) #("If you want to run as root you may have to set\n" 0 47 (:parent #157))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #150) #("You also need to set\n" 0 21 (:parent #159))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #150) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #161))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #150) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #162))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #150) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #164))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #150) #("When you get errors like:\n" 0 26 (:parent #166))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #150) #("you may need to set\n" 0 20 (:parent #168))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #148) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #151) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #154)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #154) #("s" 0 1 (:parent #159))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #154)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #161))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #154) #("plant" 0 5 (:parent #162))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #154))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #151) #("Download one database from\n" 0 27 (:parent #155))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #151) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #151) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #151) #("Check the md5sum.\n" 0 18 (:parent #158))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #151) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #159))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #151) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #161))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #151) #("and\n" 0 4 (:parent #163))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #151) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #165))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #151) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #167))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #151) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #168))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #151) #("Note for the plant database you can rename it to db" 0 51 (:parent #169)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #(", or\nchange the settings in etc/default" 0 39 (:parent #169)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #169) #("settings.py" 0 11 (:parent #176))) #("to match your path.\n" 0 20 (:parent #169)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #145))) :mode nil :granularity nil :parent #136) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #145) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #148) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #151))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #148) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #146))) :mode nil :granularity nil :parent #136) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #146) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #149) #("See " 0 4 (:parent #152)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(".\n" 0 2 (:parent #152))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #147))) :mode nil :granularity nil :parent #136) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #147) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #150) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #153)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #153))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #148))) :mode nil :granularity nil :parent #136) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #151) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #154) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #157)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #157) #("PATH" 0 4 (:parent #161))) #("and R" 0 5 (:parent #157)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #157) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #157) #("SITE" 0 4 (:parent #164))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #157))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #154)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #154) #("On one system:\n" 0 15 (:parent #159))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #154)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #154) #("and perhaps a few more.\n" 0 24 (:parent #161))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #152)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #152) #("data" 0 4 (:parent #194))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #152)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #152) #("files" 0 5 (:parent #196))) #("/genotype'" 0 10 (:parent #152))) :mode nil :granularity nil :parent #148) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #152) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #155) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #158)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #158) #("data" 0 4 (:parent #162))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #158)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #158) #("settings.py" 0 11 (:parent #164))) #("(see above in\nthis document).\n" 0 30 (:parent #158))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #155) #("You can use the GENENETWORK" 0 27 (:parent #159)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #159) #("FILES" 0 5 (:parent #163))) #("switch to set the datadir, for example\n" 0 39 (:parent #159))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #155)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #153))) :mode nil :granularity nil :parent #148) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #153) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #156) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #159))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #154))) :mode nil :granularity nil :parent #148) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #154) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #157) #("This error\n" 0 11 (:parent #160))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #157) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #162))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #157) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #163)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #163) #("LIBS" 0 4 (:parent #167))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #163) #("SITE" 0 4 (:parent #168))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #163))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #155))) :mode nil :granularity nil :parent #148) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #155) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #158) #("The following error\n" 0 20 (:parent #161))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #158) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #163))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #158) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #165))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #158) #("if that works run genenetwork after setting SQL" 0 47 (:parent #167)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #167) #("URI" 0 3 (:parent #171))) #("to something like\n" 0 18 (:parent #167))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #158))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #149))) :mode nil :granularity nil :parent #136) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #149) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #152) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #155))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #152) #("#+begin" 0 7 (:parent #156)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #156) #("src" 0 3 (:parent #160))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #156))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #152) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #157))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #152) #(" yes\n env GUIX" 0 30 (:parent #158)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #158) #("PACKAGE" 0 7 (:parent #162))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #158) #("PATH" 0 4 (:parent #163))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #158))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #152) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #159))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #152) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #160)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #164))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #160) #("PATH" 0 4 (:parent #165))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #160))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #152) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #161))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #152) #(" which should have the same HASH values " 0 48 (:parent #162)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #162) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #166))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #162)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #162)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #162)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #162) #("PACKAGE" 0 7 (:parent #172))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #162) #("PATH" 0 4 (:parent #173))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #162)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #162)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #162) #("PACKAGE" 0 7 (:parent #177))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #162) #("PATH" 0 4 (:parent #178))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #162)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #162) #("PACKAGE" 0 7 (:parent #180))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #162) #("PATH" 0 4 (:parent #181))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #162)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #162))))))) #66)) #42)) . #0)) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #13) #("NOTES" 0 5 (:parent #16))) #("\n" 0 1 (:parent #13))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #10) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #20) #("Deploying GN2 official" 0 22 (:parent #23))) #("\n" 0 1 (:parent #20))))))) "") org-export-data((plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #48))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #94) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #99) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #102) #("Large system deployments can get very " 0 38 (:parent #105)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #105) #("complex" 0 7 (:parent #109))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #111))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #106) #("GNU Guix" 0 8 (:parent #112))) #(".\n" 0 2 (:parent #106))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #102) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #107)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #107) #("GN2 Dependency Graph" 0 20 (:parent #111))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #100))) :mode nil :granularity nil :parent #94) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #100) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #103) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #106)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #106)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #106))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #101) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #104) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #107)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #107) #("default" 0 7 (:parent #111)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #111) #("settings.py" 0 11 (:parent #115)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #107))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #104) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #109))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #104) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #111))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #102))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #105))) :mode section :granularity nil :parent #102) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #105) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #108) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #111) #("Note: we moved to MariaDB" 0 25 (:parent #114))) #("\n" 0 1 (:parent #111))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #108) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #112))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #108) #("As root configure and run\n" 0 26 (:parent #113))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #108) #("If you want to run as root you may have to set\n" 0 47 (:parent #115))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #108) #("You also need to set\n" 0 21 (:parent #117))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #108) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #119))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #108) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #120))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #108) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #122))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #108) #("When you get errors like:\n" 0 26 (:parent #124))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #108)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #108) #("you may need to set\n" 0 20 (:parent #126))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #108)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #106))) :mode nil :granularity nil :parent #102) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #106) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #109) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #112)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #112) #("webqtl" 0 6 (:parent #116))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #112) #("s" 0 1 (:parent #117))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #112)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #112) #("webqtl" 0 6 (:parent #119))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #112) #("plant" 0 5 (:parent #120))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #112))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #109) #("Download one database from\n" 0 27 (:parent #113))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #109) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #("\n" 0 1 (:parent #114))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #109) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #("\n" 0 1 (:parent #115))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #109) #("Check the md5sum.\n" 0 18 (:parent #116))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #109) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #117))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #109)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #109) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #119))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #109)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #109) #("and\n" 0 4 (:parent #121))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #109)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #109) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #123))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #109)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #109) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #125))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #109) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #126))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #109) #("Note for the plant database you can rename it to db" 0 51 (:parent #127)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #127) #("webqtl" 0 6 (:parent #131))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #127) #("s" 0 1 (:parent #132))) #(", or\nchange the settings in etc/default" 0 39 (:parent #127)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #127) #("settings.py" 0 11 (:parent #134))) #("to match your path.\n" 0 20 (:parent #127)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #103) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #106) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #109))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #106) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #110)) #("\n" 0 1 (:parent #110))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #104))) :mode nil :granularity nil :parent #94) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #104) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #107) #("See " 0 4 (:parent #110)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #110)) #(".\n" 0 2 (:parent #110))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #105) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #108) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #111)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #111))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #106))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #109))) :mode section :granularity nil :parent #106) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #109) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #112) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #115)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #115) #("PATH" 0 4 (:parent #119))) #("and R" 0 5 (:parent #115)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #115) #("LIBS" 0 4 (:parent #121))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #115) #("SITE" 0 4 (:parent #122))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #115))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #112) #("On one system:\n" 0 15 (:parent #117))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #112) #("and perhaps a few more.\n" 0 24 (:parent #119))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #110)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #110) #("data" 0 4 (:parent #152))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #110)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #110) #("files" 0 5 (:parent #154))) #("/genotype'" 0 10 (:parent #110))) :mode nil :granularity nil :parent #106) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #110) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #113) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #116)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #116) #("data" 0 4 (:parent #120))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #116)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #116) #("settings.py" 0 11 (:parent #122))) #("(see above in\nthis document).\n" 0 30 (:parent #116))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #113) #("You can use the GENENETWORK" 0 27 (:parent #117)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #117) #("FILES" 0 5 (:parent #121))) #("switch to set the datadir, for example\n" 0 39 (:parent #117))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #113)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #111))) :mode nil :granularity nil :parent #106) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #111) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #114) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #117))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #112))) :mode nil :granularity nil :parent #106) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #112) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #115) #("This error\n" 0 11 (:parent #118))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #115) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #120))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #115) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #121)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #121) #("LIBS" 0 4 (:parent #125))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #121) #("SITE" 0 4 (:parent #126))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #121))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #113))) :mode nil :granularity nil :parent #106) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #113) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #116) #("The following error\n" 0 20 (:parent #119))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #116) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #121))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #116) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #123))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #116) #("if that works run genenetwork after setting SQL" 0 47 (:parent #125)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #125) #("URI" 0 3 (:parent #129))) #("to something like\n" 0 18 (:parent #125))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #116))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #107) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #110) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #113))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #110) #("#+begin" 0 7 (:parent #114)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #114) #("src" 0 3 (:parent #118))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #114))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #110) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #115))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #110) #(" yes\n env GUIX" 0 30 (:parent #116)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #116) #("PACKAGE" 0 7 (:parent #120))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #116) #("PATH" 0 4 (:parent #121))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #116))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #110) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #117))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #110) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #118)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #118) #("PACKAGE" 0 7 (:parent #122))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #118) #("PATH" 0 4 (:parent #123))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #118))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #110) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #119))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #110) #(" which should have the same HASH values " 0 48 (:parent #120)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #120) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #124))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #120)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #130))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #131))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #120)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #120)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #135))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #136))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #120)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #138))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #139))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #120))))))) #24)) #0)) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #3) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #6) #("Introduction" 0 12 (:parent #9))) #("\n" 0 1 (:parent #6)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #7) #("Install" 0 7 (:parent #10))) #("\n" 0 1 (:parent #7)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #5) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #8) #("Running GN2" 0 11 (:parent #11))) #("\n" 0 1 (:parent #8)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #9) #("Run MariaDB server" 0 18 (:parent #12))) #("\n" 0 1 (:parent #9))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #6) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #16) #("Install MariaDB with GNU GUIx" 0 29 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #17) #("Load the small database in MySQL" 0 32 (:parent #20))) #("\n" 0 1 (:parent #17)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #10) #("GN2 Dependency Graph" 0 20 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #11) #("Working with the GN2 source code" 0 32 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #12) #("Read more" 0 9 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #13) #("Trouble shooting" 0 16 (:parent #16))) #("\n" 0 1 (:parent #13))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #10) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #20) #("ImportError: No module named jinja2" 0 35 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #21) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #24)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #24) #("data" 0 4 (:parent #28))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #24)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #24) #("files" 0 5 (:parent #30))) #("/genotype'" 0 10 (:parent #24))) #("\n" 0 1 (:parent #21)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #22) #("Can't run a module" 0 18 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #23) #("Rpy2 error 'show' now found" 0 27 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #24) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #27))) #("\n" 0 1 (:parent #24)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #14) #("IRC session" 0 11 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #15) #("NOTES" 0 5 (:parent #18))) #("\n" 0 1 (:parent #15))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #12) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #22) #("Deploying GN2 official" 0 22 (:parent #25))) #("\n" 0 1 (:parent #22))))))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #48))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #94) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #99) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #102) #("Large system deployments can get very " 0 38 (:parent #105)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #105) #("complex" 0 7 (:parent #109))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #111))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #106) #("GNU Guix" 0 8 (:parent #112))) #(".\n" 0 2 (:parent #106))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #102) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #107)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #107) #("GN2 Dependency Graph" 0 20 (:parent #111))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #100))) :mode nil :granularity nil :parent #94) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #100) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #103) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #106)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #106)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #106))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #101) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #104) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #107)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #107) #("default" 0 7 (:parent #111)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #111) #("settings.py" 0 11 (:parent #115)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #107))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #104) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #109))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #104) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #111))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #102))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #105))) :mode section :granularity nil :parent #102) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #105) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #108) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #111) #("Note: we moved to MariaDB" 0 25 (:parent #114))) #("\n" 0 1 (:parent #111))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #108) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #112))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #108) #("As root configure and run\n" 0 26 (:parent #113))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #108) #("If you want to run as root you may have to set\n" 0 47 (:parent #115))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #108) #("You also need to set\n" 0 21 (:parent #117))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #108) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #119))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #108) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #120))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #108) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #122))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #108)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #108) #("When you get errors like:\n" 0 26 (:parent #124))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #108)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #108) #("you may need to set\n" 0 20 (:parent #126))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #108)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #106))) :mode nil :granularity nil :parent #102) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #106) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #109) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #112)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #112) #("webqtl" 0 6 (:parent #116))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #112) #("s" 0 1 (:parent #117))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #112)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #112) #("webqtl" 0 6 (:parent #119))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #112) #("plant" 0 5 (:parent #120))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #112))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #109) #("Download one database from\n" 0 27 (:parent #113))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #109) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #("\n" 0 1 (:parent #114))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #109) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #("\n" 0 1 (:parent #115))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #109) #("Check the md5sum.\n" 0 18 (:parent #116))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #109) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #117))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #109)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #109) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #119))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #109)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #109) #("and\n" 0 4 (:parent #121))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #109)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #109) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #123))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #109)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #109) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #125))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #109) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #126))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #109) #("Note for the plant database you can rename it to db" 0 51 (:parent #127)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #127) #("webqtl" 0 6 (:parent #131))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #127) #("s" 0 1 (:parent #132))) #(", or\nchange the settings in etc/default" 0 39 (:parent #127)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #127) #("settings.py" 0 11 (:parent #134))) #("to match your path.\n" 0 20 (:parent #127)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #103) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #106) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #109))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #106) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #110)) #("\n" 0 1 (:parent #110))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #104))) :mode nil :granularity nil :parent #94) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #104) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #107) #("See " 0 4 (:parent #110)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #110)) #(".\n" 0 2 (:parent #110))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #105) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #108) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #111)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #111))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #106))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #109))) :mode section :granularity nil :parent #106) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #109) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #112) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #115)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #115) #("PATH" 0 4 (:parent #119))) #("and R" 0 5 (:parent #115)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #115) #("LIBS" 0 4 (:parent #121))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #115) #("SITE" 0 4 (:parent #122))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #115))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #112) #("On one system:\n" 0 15 (:parent #117))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #112) #("and perhaps a few more.\n" 0 24 (:parent #119))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #110)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #110) #("data" 0 4 (:parent #152))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #110)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #110) #("files" 0 5 (:parent #154))) #("/genotype'" 0 10 (:parent #110))) :mode nil :granularity nil :parent #106) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #110) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #113) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #116)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #116) #("data" 0 4 (:parent #120))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #116)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #116) #("settings.py" 0 11 (:parent #122))) #("(see above in\nthis document).\n" 0 30 (:parent #116))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #113) #("You can use the GENENETWORK" 0 27 (:parent #117)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #117) #("FILES" 0 5 (:parent #121))) #("switch to set the datadir, for example\n" 0 39 (:parent #117))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #113)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #111))) :mode nil :granularity nil :parent #106) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #111) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #114) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #117))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #112))) :mode nil :granularity nil :parent #106) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #112) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #115) #("This error\n" 0 11 (:parent #118))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #115) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #120))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #115) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #121)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #121) #("LIBS" 0 4 (:parent #125))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #121) #("SITE" 0 4 (:parent #126))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #121))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #113))) :mode nil :granularity nil :parent #106) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #113) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #116) #("The following error\n" 0 20 (:parent #119))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #116) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #121))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #116) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #123))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #116)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #116) #("if that works run genenetwork after setting SQL" 0 47 (:parent #125)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #125) #("URI" 0 3 (:parent #129))) #("to something like\n" 0 18 (:parent #125))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #116))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #107) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #110) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #113))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #110) #("#+begin" 0 7 (:parent #114)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #114) #("src" 0 3 (:parent #118))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #114))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #110) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #115))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #110) #(" yes\n env GUIX" 0 30 (:parent #116)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #116) #("PACKAGE" 0 7 (:parent #120))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #116) #("PATH" 0 4 (:parent #121))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #116))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #110) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #117))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #110) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #118)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #118) #("PACKAGE" 0 7 (:parent #122))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #118) #("PATH" 0 4 (:parent #123))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #118))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #110) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #119))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #110) #(" which should have the same HASH values " 0 48 (:parent #120)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #120) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #124))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #120)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #120)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #120)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #130))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #131))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #120)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #120)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #135))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #136))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #120)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #120) #("PACKAGE" 0 7 (:parent #138))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #120) #("PATH" 0 4 (:parent #139))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #120)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #120))))))) #24)) #0)) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #3) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #6) #("Introduction" 0 12 (:parent #9))) #("\n" 0 1 (:parent #6)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #7) #("Install" 0 7 (:parent #10))) #("\n" 0 1 (:parent #7)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #5) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #8) #("Running GN2" 0 11 (:parent #11))) #("\n" 0 1 (:parent #8)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #9) #("Run MariaDB server" 0 18 (:parent #12))) #("\n" 0 1 (:parent #9))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #6) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #16) #("Install MariaDB with GNU GUIx" 0 29 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #17) #("Load the small database in MySQL" 0 32 (:parent #20))) #("\n" 0 1 (:parent #17)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #10) #("GN2 Dependency Graph" 0 20 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #11) #("Working with the GN2 source code" 0 32 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #12) #("Read more" 0 9 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #13) #("Trouble shooting" 0 16 (:parent #16))) #("\n" 0 1 (:parent #13))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #10) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #20) #("ImportError: No module named jinja2" 0 35 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #21) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #24)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #24) #("data" 0 4 (:parent #28))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #24)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #24) #("files" 0 5 (:parent #30))) #("/genotype'" 0 10 (:parent #24))) #("\n" 0 1 (:parent #21)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #22) #("Can't run a module" 0 18 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #23) #("Rpy2 error 'show' now found" 0 27 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #24) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #27))) #("\n" 0 1 (:parent #24)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #14) #("IRC session" 0 11 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #0) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #15) #("NOTES" 0 5 (:parent #18))) #("\n" 0 1 (:parent #15))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #12) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #22) #("Deploying GN2 official" 0 22 (:parent #25))) #("\n" 0 1 (:parent #22)))))))) mapconcat(#f(compiled-function (element) #) ((plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #49))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #95) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #98))) #49 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #100))) :mode nil :granularity nil :parent #95) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #100) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #103) #("Large system deployments can get very " 0 38 (:parent #106)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #106) #("complex" 0 7 (:parent #110))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #106)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #106) #("Guix-notes" 0 10 (:parent #112))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #106))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #103) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #107) #("Guix bioinformatics" 0 19 (:parent #111))) #("and " 0 4 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #107) #("GNU Guix" 0 8 (:parent #113))) #(".\n" 0 2 (:parent #107))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #103) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #108)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #108) #("GN2 Dependency Graph" 0 20 (:parent #112))) #(".\n" 0 2 (:parent #108))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #101))) :mode nil :granularity nil :parent #95) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #101) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #104) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #107)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #107)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #107))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #102))) :mode nil :granularity nil :parent #95) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #102) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #105) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #108)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #108) #("default" 0 7 (:parent #112)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #112) #("settings.py" 0 11 (:parent #116)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #108))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #105)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #105) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #110))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #105)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #105) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #112))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #103))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #106))) :mode section :granularity nil :parent #103) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #106) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #109) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #112) #("Note: we moved to MariaDB" 0 25 (:parent #115))) #("\n" 0 1 (:parent #112))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #109) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #113))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #109) #("As root configure and run\n" 0 26 (:parent #114))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #109)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #109) #("If you want to run as root you may have to set\n" 0 47 (:parent #116))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #109)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #109) #("You also need to set\n" 0 21 (:parent #118))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #109)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #109) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #120))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #109) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #121))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #109)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #109) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #123))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #109)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #109) #("When you get errors like:\n" 0 26 (:parent #125))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #109)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #109) #("you may need to set\n" 0 20 (:parent #127))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #109)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #107))) :mode nil :granularity nil :parent #103) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #107) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #110) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #113)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #113) #("webqtl" 0 6 (:parent #117))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #113) #("s" 0 1 (:parent #118))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #113)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #113) #("webqtl" 0 6 (:parent #120))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #113) #("plant" 0 5 (:parent #121))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #113))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #110) #("Download one database from\n" 0 27 (:parent #114))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #110) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #("\n" 0 1 (:parent #115))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #110) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\n" 0 1 (:parent #116))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #110) #("Check the md5sum.\n" 0 18 (:parent #117))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #110) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #118))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #110) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #120))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #110) #("and\n" 0 4 (:parent #122))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #110)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #110) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #124))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #110)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #110) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #126))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #110) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #127))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #110) #("Note for the plant database you can rename it to db" 0 51 (:parent #128)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #128) #("webqtl" 0 6 (:parent #132))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #128) #("s" 0 1 (:parent #133))) #(", or\nchange the settings in etc/default" 0 39 (:parent #128)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #128) #("settings.py" 0 11 (:parent #135))) #("to match your path.\n" 0 20 (:parent #128)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #104))) :mode nil :granularity nil :parent #95) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #104) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #107) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #110))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #107) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #("\n" 0 1 (:parent #111))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #105))) :mode nil :granularity nil :parent #95) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #105) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #108) #("See " 0 4 (:parent #111)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #(".\n" 0 2 (:parent #111))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #106))) :mode nil :granularity nil :parent #95) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #106) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #109) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #112)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #112)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #112))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #107))) :mode nil :granularity nil :parent #95) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #110))) :mode section :granularity nil :parent #107) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #110) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #113) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #116)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #116) #("PATH" 0 4 (:parent #120))) #("and R" 0 5 (:parent #116)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #116) #("LIBS" 0 4 (:parent #122))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #116) #("SITE" 0 4 (:parent #123))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #116))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #113)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #113) #("On one system:\n" 0 15 (:parent #118))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #113)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #113) #("and perhaps a few more.\n" 0 24 (:parent #120))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #111)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #111) #("data" 0 4 (:parent #153))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #111)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #111) #("files" 0 5 (:parent #155))) #("/genotype'" 0 10 (:parent #111))) :mode nil :granularity nil :parent #107) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #111) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #114) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #117)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #117) #("data" 0 4 (:parent #121))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #117)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #117) #("settings.py" 0 11 (:parent #123))) #("(see above in\nthis document).\n" 0 30 (:parent #117))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #114) #("You can use the GENENETWORK" 0 27 (:parent #118)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #118) #("FILES" 0 5 (:parent #122))) #("switch to set the datadir, for example\n" 0 39 (:parent #118))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #114)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #112))) :mode nil :granularity nil :parent #107) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #112) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #115) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #118))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #113))) :mode nil :granularity nil :parent #107) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #113) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #116) #("This error\n" 0 11 (:parent #119))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #116)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #116) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #121))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #116) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #122)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #122) #("LIBS" 0 4 (:parent #126))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #122) #("SITE" 0 4 (:parent #127))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #122))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #114))) :mode nil :granularity nil :parent #107) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #114) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #117) #("The following error\n" 0 20 (:parent #120))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #117)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #117) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #122))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #117)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #117) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #124))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #117)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #117) #("if that works run genenetwork after setting SQL" 0 47 (:parent #126)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #126) #("URI" 0 3 (:parent #130))) #("to something like\n" 0 18 (:parent #126))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #117))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #108))) :mode nil :granularity nil :parent #95) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #108) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #111) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #114))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #111) #("#+begin" 0 7 (:parent #115)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #115) #("src" 0 3 (:parent #119))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #115))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #111) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #116))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #111) #(" yes\n env GUIX" 0 30 (:parent #117)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #117) #("PACKAGE" 0 7 (:parent #121))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #117) #("PATH" 0 4 (:parent #122))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #117))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #111) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #118))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #111) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #119)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #119) #("PACKAGE" 0 7 (:parent #123))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #119) #("PATH" 0 4 (:parent #124))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #119))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #111) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #120))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #111) #(" which should have the same HASH values " 0 48 (:parent #121)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #121) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #125))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #121)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #121)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #121)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #131))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #132))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #121)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #121)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #136))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #137))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #121)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #121) #("PACKAGE" 0 7 (:parent #139))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #121) #("PATH" 0 4 (:parent #140))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #121)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #121))))))) #25)) . #0)) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #4) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #7) #("Introduction" 0 12 (:parent #10))) #("\n" 0 1 (:parent #7)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #5) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #8) #("Install" 0 7 (:parent #11))) #("\n" 0 1 (:parent #8)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #9) #("Running GN2" 0 11 (:parent #12))) #("\n" 0 1 (:parent #9)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #10) #("Run MariaDB server" 0 18 (:parent #13))) #("\n" 0 1 (:parent #10))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #7) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #11) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #17) #("Install MariaDB with GNU GUIx" 0 29 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #11) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #18) #("Load the small database in MySQL" 0 32 (:parent #21))) #("\n" 0 1 (:parent #18)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #11) #("GN2 Dependency Graph" 0 20 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #12) #("Working with the GN2 source code" 0 32 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #13) #("Read more" 0 9 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #14) #("Trouble shooting" 0 16 (:parent #17))) #("\n" 0 1 (:parent #14))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #11) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #15) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #21) #("ImportError: No module named jinja2" 0 35 (:parent #24))) #("\n" 0 1 (:parent #21)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #15) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #22) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #25)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #25) #("data" 0 4 (:parent #29))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #25)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #25) #("files" 0 5 (:parent #31))) #("/genotype'" 0 10 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #15) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #23) #("Can't run a module" 0 18 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #15) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #24) #("Rpy2 error 'show' now found" 0 27 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #15) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #25) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #28))) #("\n" 0 1 (:parent #25)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #15) #("IRC session" 0 11 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #1) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #16) #("NOTES" 0 5 (:parent #19))) #("\n" 0 1 (:parent #16))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #13) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #23) #("Deploying GN2 official" 0 22 (:parent #26))) #("\n" 0 1 (:parent #23)))))))) "") org-export-data((section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #70) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #73))) #24 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #75))) :mode nil :granularity nil :parent #70) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #75) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #78) #("Large system deployments can get very " 0 38 (:parent #81)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #81) #("complex" 0 7 (:parent #85))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #87))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #76) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #79) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #82)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #82)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #82))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #77))) :mode nil :granularity nil :parent #70) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #77) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #80) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #83)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #83) #("default" 0 7 (:parent #87)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #87) #("settings.py" 0 11 (:parent #91)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #83))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #80) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #85))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #80) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #87))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #78))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #81))) :mode section :granularity nil :parent #78) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #81) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #84) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #87) #("Note: we moved to MariaDB" 0 25 (:parent #90))) #("\n" 0 1 (:parent #87))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #84) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #88))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #84) #("As root configure and run\n" 0 26 (:parent #89))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #84) #("If you want to run as root you may have to set\n" 0 47 (:parent #91))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #84) #("You also need to set\n" 0 21 (:parent #93))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #84) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #95))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #84) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #96))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #84) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #98))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #84) #("When you get errors like:\n" 0 26 (:parent #100))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #84)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #84) #("you may need to set\n" 0 20 (:parent #102))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #84)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #82))) :mode nil :granularity nil :parent #78) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #82) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #85) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #88)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #88) #("webqtl" 0 6 (:parent #92))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #88) #("s" 0 1 (:parent #93))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #88)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #88) #("webqtl" 0 6 (:parent #95))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #88) #("plant" 0 5 (:parent #96))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #88))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #85) #("Download one database from\n" 0 27 (:parent #89))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #85) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #("\n" 0 1 (:parent #90))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #85) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #("\n" 0 1 (:parent #91))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #85) #("Check the md5sum.\n" 0 18 (:parent #92))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #85) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #93))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #85)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #85) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #95))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #85)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #85) #("and\n" 0 4 (:parent #97))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #85)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #85) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #99))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #85)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #85) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #101))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #85) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #102))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #85) #("Note for the plant database you can rename it to db" 0 51 (:parent #103)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #103) #("webqtl" 0 6 (:parent #107))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #103) #("s" 0 1 (:parent #108))) #(", or\nchange the settings in etc/default" 0 39 (:parent #103)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #103) #("settings.py" 0 11 (:parent #110))) #("to match your path.\n" 0 20 (:parent #103)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #79) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #82) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #85))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #82) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #86)) #("\n" 0 1 (:parent #86))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #80))) :mode nil :granularity nil :parent #70) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #80) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #83) #("See " 0 4 (:parent #86)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #86)) #(".\n" 0 2 (:parent #86))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #81) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #84) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #87)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #87))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #82))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #85))) :mode section :granularity nil :parent #82) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #85) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #88) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #91)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #91) #("PATH" 0 4 (:parent #95))) #("and R" 0 5 (:parent #91)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #91) #("LIBS" 0 4 (:parent #97))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #91) #("SITE" 0 4 (:parent #98))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #91))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #88) #("On one system:\n" 0 15 (:parent #93))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #88) #("and perhaps a few more.\n" 0 24 (:parent #95))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #86)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #86) #("data" 0 4 (:parent #128))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #86)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #86) #("files" 0 5 (:parent #130))) #("/genotype'" 0 10 (:parent #86))) :mode nil :granularity nil :parent #82) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #86) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #89) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #92)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #92) #("data" 0 4 (:parent #96))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #92)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #92) #("settings.py" 0 11 (:parent #98))) #("(see above in\nthis document).\n" 0 30 (:parent #92))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #89) #("You can use the GENENETWORK" 0 27 (:parent #93)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #93) #("FILES" 0 5 (:parent #97))) #("switch to set the datadir, for example\n" 0 39 (:parent #93))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #89)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #87))) :mode nil :granularity nil :parent #82) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #87) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #90) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #93))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #88))) :mode nil :granularity nil :parent #82) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #88) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #91) #("This error\n" 0 11 (:parent #94))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #91) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #96))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #91) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #97)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #97) #("LIBS" 0 4 (:parent #101))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #97) #("SITE" 0 4 (:parent #102))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #97))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #89))) :mode nil :granularity nil :parent #82) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #89) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #92) #("The following error\n" 0 20 (:parent #95))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #92) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #97))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #92) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #99))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #92) #("if that works run genenetwork after setting SQL" 0 47 (:parent #101)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #101) #("URI" 0 3 (:parent #105))) #("to something like\n" 0 18 (:parent #101))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #92))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #83) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #86) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #89))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #86) #("#+begin" 0 7 (:parent #90)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #90) #("src" 0 3 (:parent #94))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #90))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #86) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #91))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #86) #(" yes\n env GUIX" 0 30 (:parent #92)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #92) #("PACKAGE" 0 7 (:parent #96))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #92) #("PATH" 0 4 (:parent #97))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #92))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #86) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #93))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #86) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #94)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #94) #("PACKAGE" 0 7 (:parent #98))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #94) #("PATH" 0 4 (:parent #99))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #94))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #86) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #95))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #86) #(" which should have the same HASH values " 0 48 (:parent #96)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #96) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #100))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #96)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #106))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #107))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #96)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #96)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #111))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #112))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #96)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #115))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #96))))))) #0)) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #0) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #9) #("Introduction" 0 12 (:parent #12))) #("\n" 0 1 (:parent #9)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #10) #("Install" 0 7 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #11) #("Running GN2" 0 11 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #12) #("Run MariaDB server" 0 18 (:parent #15))) #("\n" 0 1 (:parent #12))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #9) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #19) #("Install MariaDB with GNU GUIx" 0 29 (:parent #22))) #("\n" 0 1 (:parent #19)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #20) #("Load the small database in MySQL" 0 32 (:parent #23))) #("\n" 0 1 (:parent #20)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #13) #("GN2 Dependency Graph" 0 20 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #14) #("Working with the GN2 source code" 0 32 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #15) #("Read more" 0 9 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #16) #("Trouble shooting" 0 16 (:parent #19))) #("\n" 0 1 (:parent #16))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #13) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #23) #("ImportError: No module named jinja2" 0 35 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #24) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #27)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #27) #("data" 0 4 (:parent #31))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #27)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #27) #("files" 0 5 (:parent #33))) #("/genotype'" 0 10 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #25) #("Can't run a module" 0 18 (:parent #28))) #("\n" 0 1 (:parent #25)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #26) #("Rpy2 error 'show' now found" 0 27 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #27) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #30))) #("\n" 0 1 (:parent #27)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #17) #("IRC session" 0 11 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #18) #("NOTES" 0 5 (:parent #21))) #("\n" 0 1 (:parent #18))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #15) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #19) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #25) #("Deploying GN2 official" 0 22 (:parent #28))) #("\n" 0 1 (:parent #25)))))))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #70) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #73))) #24 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #75))) :mode nil :granularity nil :parent #70) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #75) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #78) #("Large system deployments can get very " 0 38 (:parent #81)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #81) #("complex" 0 7 (:parent #85))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #87))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #76) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #79) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #82)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #82)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #82))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #77))) :mode nil :granularity nil :parent #70) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #77) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #80) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #83)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #83) #("default" 0 7 (:parent #87)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #87) #("settings.py" 0 11 (:parent #91)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #83))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #80) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #85))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #80) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #87))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #78))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #81))) :mode section :granularity nil :parent #78) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #81) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #84) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #87) #("Note: we moved to MariaDB" 0 25 (:parent #90))) #("\n" 0 1 (:parent #87))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #84) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #88))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #84) #("As root configure and run\n" 0 26 (:parent #89))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #84) #("If you want to run as root you may have to set\n" 0 47 (:parent #91))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #84) #("You also need to set\n" 0 21 (:parent #93))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #84) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #95))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #84) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #96))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #84) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #98))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #84)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #84) #("When you get errors like:\n" 0 26 (:parent #100))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #84)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #84) #("you may need to set\n" 0 20 (:parent #102))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #84)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #82))) :mode nil :granularity nil :parent #78) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #82) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #85) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #88)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #88) #("webqtl" 0 6 (:parent #92))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #88) #("s" 0 1 (:parent #93))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #88)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #88) #("webqtl" 0 6 (:parent #95))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #88) #("plant" 0 5 (:parent #96))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #88))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #85) #("Download one database from\n" 0 27 (:parent #89))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #85) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #("\n" 0 1 (:parent #90))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #85) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #("\n" 0 1 (:parent #91))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #85) #("Check the md5sum.\n" 0 18 (:parent #92))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #85) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #93))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #85)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #85) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #95))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #85)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #85) #("and\n" 0 4 (:parent #97))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #85)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #85) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #99))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #85)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #85) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #101))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #85) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #102))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #85) #("Note for the plant database you can rename it to db" 0 51 (:parent #103)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #103) #("webqtl" 0 6 (:parent #107))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #103) #("s" 0 1 (:parent #108))) #(", or\nchange the settings in etc/default" 0 39 (:parent #103)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #103) #("settings.py" 0 11 (:parent #110))) #("to match your path.\n" 0 20 (:parent #103)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #79) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #82) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #85))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #82) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #86)) #("\n" 0 1 (:parent #86))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #80))) :mode nil :granularity nil :parent #70) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #80) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #83) #("See " 0 4 (:parent #86)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #86)) #(".\n" 0 2 (:parent #86))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #81) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #84) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #87)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #87))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #82))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #85))) :mode section :granularity nil :parent #82) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #85) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #88) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #91)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #91) #("PATH" 0 4 (:parent #95))) #("and R" 0 5 (:parent #91)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #91) #("LIBS" 0 4 (:parent #97))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #91) #("SITE" 0 4 (:parent #98))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #91))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #88) #("On one system:\n" 0 15 (:parent #93))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #88) #("and perhaps a few more.\n" 0 24 (:parent #95))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #86)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #86) #("data" 0 4 (:parent #128))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #86)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #86) #("files" 0 5 (:parent #130))) #("/genotype'" 0 10 (:parent #86))) :mode nil :granularity nil :parent #82) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #86) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #89) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #92)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #92) #("data" 0 4 (:parent #96))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #92)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #92) #("settings.py" 0 11 (:parent #98))) #("(see above in\nthis document).\n" 0 30 (:parent #92))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #89) #("You can use the GENENETWORK" 0 27 (:parent #93)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #93) #("FILES" 0 5 (:parent #97))) #("switch to set the datadir, for example\n" 0 39 (:parent #93))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #89)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #87))) :mode nil :granularity nil :parent #82) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #87) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #90) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #93))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #88))) :mode nil :granularity nil :parent #82) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #88) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #91) #("This error\n" 0 11 (:parent #94))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #91) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #96))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #91) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #97)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #97) #("LIBS" 0 4 (:parent #101))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #97) #("SITE" 0 4 (:parent #102))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #97))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #89))) :mode nil :granularity nil :parent #82) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #89) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #92) #("The following error\n" 0 20 (:parent #95))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #92) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #97))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #92) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #99))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #92)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #92) #("if that works run genenetwork after setting SQL" 0 47 (:parent #101)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #101) #("URI" 0 3 (:parent #105))) #("to something like\n" 0 18 (:parent #101))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #92))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #83) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #86) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #89))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #86) #("#+begin" 0 7 (:parent #90)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #90) #("src" 0 3 (:parent #94))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #90))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #86) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #91))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #86) #(" yes\n env GUIX" 0 30 (:parent #92)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #92) #("PACKAGE" 0 7 (:parent #96))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #92) #("PATH" 0 4 (:parent #97))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #92))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #86) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #93))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #86) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #94)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #94) #("PACKAGE" 0 7 (:parent #98))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #94) #("PATH" 0 4 (:parent #99))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #94))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #86) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #95))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #86) #(" which should have the same HASH values " 0 48 (:parent #96)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #96) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #100))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #96)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #96)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #96)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #106))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #107))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #96)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #96)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #111))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #112))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #96)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #96) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #96) #("PATH" 0 4 (:parent #115))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #96)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #96)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #96))))))) #0)) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #0) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #6) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #9) #("Introduction" 0 12 (:parent #12))) #("\n" 0 1 (:parent #9)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #10) #("Install" 0 7 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #11) #("Running GN2" 0 11 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #12) #("Run MariaDB server" 0 18 (:parent #15))) #("\n" 0 1 (:parent #12))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #9) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #19) #("Install MariaDB with GNU GUIx" 0 29 (:parent #22))) #("\n" 0 1 (:parent #19)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #20) #("Load the small database in MySQL" 0 32 (:parent #23))) #("\n" 0 1 (:parent #20)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #13) #("GN2 Dependency Graph" 0 20 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #14) #("Working with the GN2 source code" 0 32 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #15) #("Read more" 0 9 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #16) #("Trouble shooting" 0 16 (:parent #19))) #("\n" 0 1 (:parent #16))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #13) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #23) #("ImportError: No module named jinja2" 0 35 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #24) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #27)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #27) #("data" 0 4 (:parent #31))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #27)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #27) #("files" 0 5 (:parent #33))) #("/genotype'" 0 10 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #25) #("Can't run a module" 0 18 (:parent #28))) #("\n" 0 1 (:parent #25)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #26) #("Rpy2 error 'show' now found" 0 27 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #17) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #27) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #30))) #("\n" 0 1 (:parent #27)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #17) #("IRC session" 0 11 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #3) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #18) #("NOTES" 0 5 (:parent #21))) #("\n" 0 1 (:parent #18))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #15) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #19) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #25) #("Deploying GN2 official" 0 22 (:parent #28))) #("\n" 0 1 (:parent #25))))))))) mapconcat(#f(compiled-function (element) #) ((section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #25))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #71) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #74))) #25 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #76))) :mode nil :granularity nil :parent #71) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #76) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #79) #("Large system deployments can get very " 0 38 (:parent #82)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #82) #("complex" 0 7 (:parent #86))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #82)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #82) #("Guix-notes" 0 10 (:parent #88))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #82))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #79) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #83) #("Guix bioinformatics" 0 19 (:parent #87))) #("and " 0 4 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #83) #("GNU Guix" 0 8 (:parent #89))) #(".\n" 0 2 (:parent #83))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #79) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #84)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #84) #("GN2 Dependency Graph" 0 20 (:parent #88))) #(".\n" 0 2 (:parent #84))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #77))) :mode nil :granularity nil :parent #71) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #77) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #80) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #83)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #83)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #83))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #78))) :mode nil :granularity nil :parent #71) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #78) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #81) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #84)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #84) #("default" 0 7 (:parent #88)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #88) #("settings.py" 0 11 (:parent #92)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #84))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #81)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #81) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #86))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #81)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #81) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #88))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #79))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #82))) :mode section :granularity nil :parent #79) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #82) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #85) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #88) #("Note: we moved to MariaDB" 0 25 (:parent #91))) #("\n" 0 1 (:parent #88))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #85) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #89))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #85) #("As root configure and run\n" 0 26 (:parent #90))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #85)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #85) #("If you want to run as root you may have to set\n" 0 47 (:parent #92))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #85)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #85) #("You also need to set\n" 0 21 (:parent #94))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #85)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #85) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #96))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #85) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #97))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #85)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #85) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #99))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #85)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #85) #("When you get errors like:\n" 0 26 (:parent #101))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #85)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #85) #("you may need to set\n" 0 20 (:parent #103))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #85)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #83))) :mode nil :granularity nil :parent #79) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #83) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #86) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #89)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #89) #("webqtl" 0 6 (:parent #93))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #89) #("s" 0 1 (:parent #94))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #89)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #89) #("webqtl" 0 6 (:parent #96))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #89) #("plant" 0 5 (:parent #97))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #89))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #86) #("Download one database from\n" 0 27 (:parent #90))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #86) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #("\n" 0 1 (:parent #91))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #86) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\n" 0 1 (:parent #92))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #86) #("Check the md5sum.\n" 0 18 (:parent #93))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #86) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #94))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #86) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #96))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #86) #("and\n" 0 4 (:parent #98))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #86)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #86) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #100))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #86)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #86) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #102))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #86) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #103))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #86) #("Note for the plant database you can rename it to db" 0 51 (:parent #104)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #104) #("webqtl" 0 6 (:parent #108))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #104) #("s" 0 1 (:parent #109))) #(", or\nchange the settings in etc/default" 0 39 (:parent #104)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #104) #("settings.py" 0 11 (:parent #111))) #("to match your path.\n" 0 20 (:parent #104)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #80))) :mode nil :granularity nil :parent #71) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #80) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #83) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #86))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #83) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #("\n" 0 1 (:parent #87))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #81))) :mode nil :granularity nil :parent #71) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #81) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #84) #("See " 0 4 (:parent #87)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #(".\n" 0 2 (:parent #87))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #82))) :mode nil :granularity nil :parent #71) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #82) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #85) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #88)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #88)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #88))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #83))) :mode nil :granularity nil :parent #71) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #86))) :mode section :granularity nil :parent #83) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #86) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #89) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #92)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #92) #("PATH" 0 4 (:parent #96))) #("and R" 0 5 (:parent #92)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #92) #("LIBS" 0 4 (:parent #98))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #92) #("SITE" 0 4 (:parent #99))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #92))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #89)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #89) #("On one system:\n" 0 15 (:parent #94))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #89)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #89) #("and perhaps a few more.\n" 0 24 (:parent #96))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #87)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #87) #("data" 0 4 (:parent #129))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #87)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #87) #("files" 0 5 (:parent #131))) #("/genotype'" 0 10 (:parent #87))) :mode nil :granularity nil :parent #83) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #87) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #90) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #93)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #93) #("data" 0 4 (:parent #97))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #93)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #93) #("settings.py" 0 11 (:parent #99))) #("(see above in\nthis document).\n" 0 30 (:parent #93))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #90) #("You can use the GENENETWORK" 0 27 (:parent #94)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #94) #("FILES" 0 5 (:parent #98))) #("switch to set the datadir, for example\n" 0 39 (:parent #94))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #90)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #88))) :mode nil :granularity nil :parent #83) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #88) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #91) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #94))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #89))) :mode nil :granularity nil :parent #83) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #89) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #92) #("This error\n" 0 11 (:parent #95))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #92)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #92) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #97))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #92) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #98)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #98) #("LIBS" 0 4 (:parent #102))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #98) #("SITE" 0 4 (:parent #103))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #98))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #90))) :mode nil :granularity nil :parent #83) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #90) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #93) #("The following error\n" 0 20 (:parent #96))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #93)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #93) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #98))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #93)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #93) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #100))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #93)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #93) #("if that works run genenetwork after setting SQL" 0 47 (:parent #102)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #102) #("URI" 0 3 (:parent #106))) #("to something like\n" 0 18 (:parent #102))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #93))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #84))) :mode nil :granularity nil :parent #71) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #84) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #87) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #90))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #87) #("#+begin" 0 7 (:parent #91)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #91) #("src" 0 3 (:parent #95))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #91))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #87) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #92))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #87) #(" yes\n env GUIX" 0 30 (:parent #93)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #93) #("PACKAGE" 0 7 (:parent #97))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #93) #("PATH" 0 4 (:parent #98))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #93))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #87) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #94))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #87) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #95)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #95) #("PACKAGE" 0 7 (:parent #99))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #95) #("PATH" 0 4 (:parent #100))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #95))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #87) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #96))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #87) #(" which should have the same HASH values " 0 48 (:parent #97)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #97) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #101))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #97)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #97)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #97)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #107))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #108))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #97)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #97)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #112))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #113))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #97)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #97) #("PACKAGE" 0 7 (:parent #115))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #97) #("PATH" 0 4 (:parent #116))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #97)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #97)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #97))))))) . #0)) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #1) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #7) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #10) #("Introduction" 0 12 (:parent #13))) #("\n" 0 1 (:parent #10)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #11) #("Install" 0 7 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #12) #("Running GN2" 0 11 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #13) #("Run MariaDB server" 0 18 (:parent #16))) #("\n" 0 1 (:parent #13))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #10) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #20) #("Install MariaDB with GNU GUIx" 0 29 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #14) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #21) #("Load the small database in MySQL" 0 32 (:parent #24))) #("\n" 0 1 (:parent #21)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #14) #("GN2 Dependency Graph" 0 20 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #15) #("Working with the GN2 source code" 0 32 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #16) #("Read more" 0 9 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #17) #("Trouble shooting" 0 16 (:parent #20))) #("\n" 0 1 (:parent #17))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #14) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #24) #("ImportError: No module named jinja2" 0 35 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #25) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #28)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #28) #("data" 0 4 (:parent #32))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #28)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #28) #("files" 0 5 (:parent #34))) #("/genotype'" 0 10 (:parent #28))) #("\n" 0 1 (:parent #25)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #26) #("Can't run a module" 0 18 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #27) #("Rpy2 error 'show' now found" 0 27 (:parent #30))) #("\n" 0 1 (:parent #27)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #28) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #31))) #("\n" 0 1 (:parent #28)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #18) #("IRC session" 0 11 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #4) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #19) #("NOTES" 0 5 (:parent #22))) #("\n" 0 1 (:parent #19))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #16) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #26) #("Deploying GN2 official" 0 22 (:parent #29))) #("\n" 0 1 (:parent #26))))))))) "") org-export-data((headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #0))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #46) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #49))) #0 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #51) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #54) #("Large system deployments can get very " 0 38 (:parent #57)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #57) #("complex" 0 7 (:parent #61))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #63))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #58) #("GNU Guix" 0 8 (:parent #64))) #(".\n" 0 2 (:parent #58))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #54) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #59)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #59) #("GN2 Dependency Graph" 0 20 (:parent #63))) #(".\n" 0 2 (:parent #59))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #52) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #55) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #58)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #58)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #58))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #53))) :mode nil :granularity nil :parent #46) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #53) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #56) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #59)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #59) #("default" 0 7 (:parent #63)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #63) #("settings.py" 0 11 (:parent #67)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #59))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #56) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #61))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #56) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #63))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #54))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #57))) :mode section :granularity nil :parent #54) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #57) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #60) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #63) #("Note: we moved to MariaDB" 0 25 (:parent #66))) #("\n" 0 1 (:parent #63))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #60) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #64))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #60) #("As root configure and run\n" 0 26 (:parent #65))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #60) #("If you want to run as root you may have to set\n" 0 47 (:parent #67))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #60) #("You also need to set\n" 0 21 (:parent #69))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #60) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #71))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #60) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #72))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #60) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #74))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #60) #("When you get errors like:\n" 0 26 (:parent #76))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #60)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #60) #("you may need to set\n" 0 20 (:parent #78))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #60)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #58))) :mode nil :granularity nil :parent #54) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #58) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #61) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #64)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #64) #("webqtl" 0 6 (:parent #68))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #64) #("s" 0 1 (:parent #69))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #64)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #64) #("webqtl" 0 6 (:parent #71))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #64) #("plant" 0 5 (:parent #72))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #64))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #61) #("Download one database from\n" 0 27 (:parent #65))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #61) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #66)) #("\n" 0 1 (:parent #66))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #61) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #("\n" 0 1 (:parent #67))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #61) #("Check the md5sum.\n" 0 18 (:parent #68))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #61) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #69))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #61)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #61) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #71))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #61)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #61) #("and\n" 0 4 (:parent #73))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #61)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #61) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #75))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #61)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #61) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #77))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #61) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #78))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #61) #("Note for the plant database you can rename it to db" 0 51 (:parent #79)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #79) #("webqtl" 0 6 (:parent #83))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #79) #("s" 0 1 (:parent #84))) #(", or\nchange the settings in etc/default" 0 39 (:parent #79)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #79) #("settings.py" 0 11 (:parent #86))) #("to match your path.\n" 0 20 (:parent #79)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #55) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #58) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #61))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #58) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #62)) #("\n" 0 1 (:parent #62))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #56))) :mode nil :granularity nil :parent #46) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #56) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #59) #("See " 0 4 (:parent #62)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #62)) #(".\n" 0 2 (:parent #62))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #57) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #60) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #63)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #63))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #58))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #61))) :mode section :granularity nil :parent #58) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #61) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #64) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #67)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #67) #("PATH" 0 4 (:parent #71))) #("and R" 0 5 (:parent #67)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #67) #("LIBS" 0 4 (:parent #73))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #67) #("SITE" 0 4 (:parent #74))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #67))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #64) #("On one system:\n" 0 15 (:parent #69))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #64) #("and perhaps a few more.\n" 0 24 (:parent #71))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #62)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #62) #("data" 0 4 (:parent #104))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #62)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #62) #("files" 0 5 (:parent #106))) #("/genotype'" 0 10 (:parent #62))) :mode nil :granularity nil :parent #58) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #62) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #65) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #68)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #68) #("data" 0 4 (:parent #72))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #68)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #68) #("settings.py" 0 11 (:parent #74))) #("(see above in\nthis document).\n" 0 30 (:parent #68))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #65) #("You can use the GENENETWORK" 0 27 (:parent #69)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #69) #("FILES" 0 5 (:parent #73))) #("switch to set the datadir, for example\n" 0 39 (:parent #69))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #65)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #63))) :mode nil :granularity nil :parent #58) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #63) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #66) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #69))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #64))) :mode nil :granularity nil :parent #58) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #64) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #67) #("This error\n" 0 11 (:parent #70))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #67) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #72))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #67) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #73)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #73) #("LIBS" 0 4 (:parent #77))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #73) #("SITE" 0 4 (:parent #78))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #73))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #65))) :mode nil :granularity nil :parent #58) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #65) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #68) #("The following error\n" 0 20 (:parent #71))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #68) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #73))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #68) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #75))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #68) #("if that works run genenetwork after setting SQL" 0 47 (:parent #77)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #77) #("URI" 0 3 (:parent #81))) #("to something like\n" 0 18 (:parent #77))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #68))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #59) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #62) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #65))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #62) #("#+begin" 0 7 (:parent #66)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #66) #("src" 0 3 (:parent #70))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #66))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #62) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #67))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #62) #(" yes\n env GUIX" 0 30 (:parent #68)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #68) #("PACKAGE" 0 7 (:parent #72))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #68) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #68))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #62) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #69))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #62) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #70)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #70) #("PACKAGE" 0 7 (:parent #74))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #70) #("PATH" 0 4 (:parent #75))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #70))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #62) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #71))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #62) #(" which should have the same HASH values " 0 48 (:parent #72)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #72) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #76))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #72)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #82))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #83))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #72)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #72)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #87))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #88))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #72)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #91))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #72))))))) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #0) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #3) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #12) #("Introduction" 0 12 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #13) #("Install" 0 7 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #14) #("Running GN2" 0 11 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #15) #("Run MariaDB server" 0 18 (:parent #18))) #("\n" 0 1 (:parent #15))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #12) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #22) #("Install MariaDB with GNU GUIx" 0 29 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #23) #("Load the small database in MySQL" 0 32 (:parent #26))) #("\n" 0 1 (:parent #23)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #16) #("GN2 Dependency Graph" 0 20 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #17) #("Working with the GN2 source code" 0 32 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #18) #("Read more" 0 9 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #19) #("Trouble shooting" 0 16 (:parent #22))) #("\n" 0 1 (:parent #19))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #16) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #26) #("ImportError: No module named jinja2" 0 35 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #27) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #30)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #30) #("data" 0 4 (:parent #34))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #30)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #30) #("files" 0 5 (:parent #36))) #("/genotype'" 0 10 (:parent #30))) #("\n" 0 1 (:parent #27)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #28) #("Can't run a module" 0 18 (:parent #31))) #("\n" 0 1 (:parent #28)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #26) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #29) #("Rpy2 error 'show' now found" 0 27 (:parent #32))) #("\n" 0 1 (:parent #29)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #27) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #30) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #33))) #("\n" 0 1 (:parent #30)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #20) #("IRC session" 0 11 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #21) #("NOTES" 0 5 (:parent #24))) #("\n" 0 1 (:parent #21))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #18) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #28) #("Deploying GN2 official" 0 22 (:parent #31))) #("\n" 0 1 (:parent #28))))))))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #0))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #46) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #49))) #0 (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #51) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #54) #("Large system deployments can get very " 0 38 (:parent #57)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #57) #("complex" 0 7 (:parent #61))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #63))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #58) #("GNU Guix" 0 8 (:parent #64))) #(".\n" 0 2 (:parent #58))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #54) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #59)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #59) #("GN2 Dependency Graph" 0 20 (:parent #63))) #(".\n" 0 2 (:parent #59))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #52) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #55) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #58)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #58)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #58))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #53))) :mode nil :granularity nil :parent #46) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #53) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #56) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #59)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #59) #("default" 0 7 (:parent #63)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #63) #("settings.py" 0 11 (:parent #67)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #59))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #56) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #61))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #56) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #63))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #54))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #57))) :mode section :granularity nil :parent #54) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #57) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #60) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #63) #("Note: we moved to MariaDB" 0 25 (:parent #66))) #("\n" 0 1 (:parent #63))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #60) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #64))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #60) #("As root configure and run\n" 0 26 (:parent #65))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #60) #("If you want to run as root you may have to set\n" 0 47 (:parent #67))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #60) #("You also need to set\n" 0 21 (:parent #69))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #60) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #71))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #60) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #72))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #60) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #74))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #60)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #60) #("When you get errors like:\n" 0 26 (:parent #76))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #60)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #60) #("you may need to set\n" 0 20 (:parent #78))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #60)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #58))) :mode nil :granularity nil :parent #54) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #58) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #61) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #64)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #64) #("webqtl" 0 6 (:parent #68))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #64) #("s" 0 1 (:parent #69))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #64)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #64) #("webqtl" 0 6 (:parent #71))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #64) #("plant" 0 5 (:parent #72))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #64))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #61) #("Download one database from\n" 0 27 (:parent #65))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #61) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #66)) #("\n" 0 1 (:parent #66))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #61) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #("\n" 0 1 (:parent #67))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #61) #("Check the md5sum.\n" 0 18 (:parent #68))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #61) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #69))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #61)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #61) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #71))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #61)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #61) #("and\n" 0 4 (:parent #73))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #61)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #61) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #75))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #61)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #61) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #77))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #61) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #78))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #61) #("Note for the plant database you can rename it to db" 0 51 (:parent #79)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #79) #("webqtl" 0 6 (:parent #83))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #79) #("s" 0 1 (:parent #84))) #(", or\nchange the settings in etc/default" 0 39 (:parent #79)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #79) #("settings.py" 0 11 (:parent #86))) #("to match your path.\n" 0 20 (:parent #79)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #55) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #58) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #61))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #58) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #62)) #("\n" 0 1 (:parent #62))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #56))) :mode nil :granularity nil :parent #46) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #56) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #59) #("See " 0 4 (:parent #62)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #62)) #(".\n" 0 2 (:parent #62))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #57) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #60) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #63)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #63))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #58))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #61))) :mode section :granularity nil :parent #58) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #61) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #64) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #67)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #67) #("PATH" 0 4 (:parent #71))) #("and R" 0 5 (:parent #67)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #67) #("LIBS" 0 4 (:parent #73))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #67) #("SITE" 0 4 (:parent #74))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #67))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #64) #("On one system:\n" 0 15 (:parent #69))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #64) #("and perhaps a few more.\n" 0 24 (:parent #71))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #62)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #62) #("data" 0 4 (:parent #104))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #62)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #62) #("files" 0 5 (:parent #106))) #("/genotype'" 0 10 (:parent #62))) :mode nil :granularity nil :parent #58) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #62) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #65) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #68)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #68) #("data" 0 4 (:parent #72))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #68)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #68) #("settings.py" 0 11 (:parent #74))) #("(see above in\nthis document).\n" 0 30 (:parent #68))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #65) #("You can use the GENENETWORK" 0 27 (:parent #69)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #69) #("FILES" 0 5 (:parent #73))) #("switch to set the datadir, for example\n" 0 39 (:parent #69))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #65)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #63))) :mode nil :granularity nil :parent #58) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #63) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #66) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #69))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #64))) :mode nil :granularity nil :parent #58) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #64) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #67) #("This error\n" 0 11 (:parent #70))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #67) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #72))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #67) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #73)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #73) #("LIBS" 0 4 (:parent #77))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #73) #("SITE" 0 4 (:parent #78))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #73))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #65))) :mode nil :granularity nil :parent #58) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #65) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #68) #("The following error\n" 0 20 (:parent #71))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #68) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #73))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #68) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #75))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #68)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #68) #("if that works run genenetwork after setting SQL" 0 47 (:parent #77)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #77) #("URI" 0 3 (:parent #81))) #("to something like\n" 0 18 (:parent #77))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #68))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #59) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #62) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #65))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #62) #("#+begin" 0 7 (:parent #66)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #66) #("src" 0 3 (:parent #70))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #66))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #62) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #67))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #62) #(" yes\n env GUIX" 0 30 (:parent #68)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #68) #("PACKAGE" 0 7 (:parent #72))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #68) #("PATH" 0 4 (:parent #73))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #68))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #62) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #69))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #62) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #70)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #70) #("PACKAGE" 0 7 (:parent #74))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #70) #("PATH" 0 4 (:parent #75))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #70))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #62) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #71))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #62) #(" which should have the same HASH values " 0 48 (:parent #72)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #72) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #76))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #72)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #72)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #72)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #82))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #83))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #72)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #72)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #87))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #88))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #72)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #72) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #72) #("PATH" 0 4 (:parent #91))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #72)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #72)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #72))))))) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #0) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #3) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #12) #("Introduction" 0 12 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #10) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #13) #("Install" 0 7 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #14) #("Running GN2" 0 11 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #15) #("Run MariaDB server" 0 18 (:parent #18))) #("\n" 0 1 (:parent #15))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #12) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #22) #("Install MariaDB with GNU GUIx" 0 29 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #16) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #23) #("Load the small database in MySQL" 0 32 (:parent #26))) #("\n" 0 1 (:parent #23)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #16) #("GN2 Dependency Graph" 0 20 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #17) #("Working with the GN2 source code" 0 32 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #18) #("Read more" 0 9 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #19) #("Trouble shooting" 0 16 (:parent #22))) #("\n" 0 1 (:parent #19))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #16) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #26) #("ImportError: No module named jinja2" 0 35 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #27) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #30)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #30) #("data" 0 4 (:parent #34))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #30)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #30) #("files" 0 5 (:parent #36))) #("/genotype'" 0 10 (:parent #30))) #("\n" 0 1 (:parent #27)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #28) #("Can't run a module" 0 18 (:parent #31))) #("\n" 0 1 (:parent #28)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #26) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #29) #("Rpy2 error 'show' now found" 0 27 (:parent #32))) #("\n" 0 1 (:parent #29)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #27) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #30) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #33))) #("\n" 0 1 (:parent #30)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #20) #("IRC session" 0 11 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #6) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #21) #("NOTES" 0 5 (:parent #24))) #("\n" 0 1 (:parent #21))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #18) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #28) #("Deploying GN2 official" 0 22 (:parent #31))) #("\n" 0 1 (:parent #28)))))))))) mapconcat(#f(compiled-function (element) #) ((section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #1))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #2))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #2) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #5) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #11) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #14) #("Introduction" 0 12 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #12) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #15) #("Install" 0 7 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #16) #("Running GN2" 0 11 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #17) #("Run MariaDB server" 0 18 (:parent #20))) #("\n" 0 1 (:parent #17))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #14) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #24) #("Install MariaDB with GNU GUIx" 0 29 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #18) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #25) #("Load the small database in MySQL" 0 32 (:parent #28))) #("\n" 0 1 (:parent #25)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #18) #("GN2 Dependency Graph" 0 20 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #19) #("Working with the GN2 source code" 0 32 (:parent #22))) #("\n" 0 1 (:parent #19)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #20) #("Read more" 0 9 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #21) #("Trouble shooting" 0 16 (:parent #24))) #("\n" 0 1 (:parent #21))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #18) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #25) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #28) #("ImportError: No module named jinja2" 0 35 (:parent #31))) #("\n" 0 1 (:parent #28)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #26) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #29) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #32)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #32) #("data" 0 4 (:parent #36))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #32)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #32) #("files" 0 5 (:parent #38))) #("/genotype'" 0 10 (:parent #32))) #("\n" 0 1 (:parent #29)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #27) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #30) #("Can't run a module" 0 18 (:parent #33))) #("\n" 0 1 (:parent #30)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #28) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #31) #("Rpy2 error 'show' now found" 0 27 (:parent #34))) #("\n" 0 1 (:parent #31)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #22) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #29) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #32) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #35))) #("\n" 0 1 (:parent #32)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #22) #("IRC session" 0 11 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #8) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #23) #("NOTES" 0 5 (:parent #26))) #("\n" 0 1 (:parent #23))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #20) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #27) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #30) #("Deploying GN2 official" 0 22 (:parent #33))) #("\n" 0 1 (:parent #30))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #3))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #3) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #6) #("Large system deployments can get very " 0 38 (:parent #9)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #9) #("complex" 0 7 (:parent #13))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #9)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #9) #("Guix-notes" 0 10 (:parent #15))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #9))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #6) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #10)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #10) #("Guix bioinformatics" 0 19 (:parent #14))) #("and " 0 4 (:parent #10)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #10) #("GNU Guix" 0 8 (:parent #16))) #(".\n" 0 2 (:parent #10))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #6) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #11)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #11) #("GN2 Dependency Graph" 0 20 (:parent #15))) #(".\n" 0 2 (:parent #11))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #4))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #4) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #7) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #10)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #10)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #10))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #5))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #5) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #8) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #11)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #11) #("default" 0 7 (:parent #15)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #15) #("settings.py" 0 11 (:parent #19)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #11))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #8)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #8) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #13))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #8)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #8) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #15))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #6))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #9))) :mode section :granularity nil :parent #6) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #9) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #12) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #15) #("Note: we moved to MariaDB" 0 25 (:parent #18))) #("\n" 0 1 (:parent #15))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #12) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #16))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #12) #("As root configure and run\n" 0 26 (:parent #17))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #12)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #12) #("If you want to run as root you may have to set\n" 0 47 (:parent #19))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #12)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #12) #("You also need to set\n" 0 21 (:parent #21))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #12)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #12) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #23))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #12) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #24))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #12)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #12) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #26))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #12)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #12) #("When you get errors like:\n" 0 26 (:parent #28))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #12)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #12) #("you may need to set\n" 0 20 (:parent #30))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #12)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #10))) :mode nil :granularity nil :parent #6) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #10) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #13) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #16)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #16) #("webqtl" 0 6 (:parent #20))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #16) #("s" 0 1 (:parent #21))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #16)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #16) #("webqtl" 0 6 (:parent #23))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #16) #("plant" 0 5 (:parent #24))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #16))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #13) #("Download one database from\n" 0 27 (:parent #17))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #13) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #18)) #("\n" 0 1 (:parent #18))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #13) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #("\n" 0 1 (:parent #19))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #13) #("Check the md5sum.\n" 0 18 (:parent #20))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #13) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #21))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #13)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #13) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #23))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #13)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #13) #("and\n" 0 4 (:parent #25))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #13)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #13) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #27))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #13)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #13) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #29))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #13) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #30))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #13) #("Note for the plant database you can rename it to db" 0 51 (:parent #31)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #31) #("webqtl" 0 6 (:parent #35))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #31) #("s" 0 1 (:parent #36))) #(", or\nchange the settings in etc/default" 0 39 (:parent #31)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #31) #("settings.py" 0 11 (:parent #38))) #("to match your path.\n" 0 20 (:parent #31)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #7))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #7) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #10) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #13))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #10) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #14)) #("\n" 0 1 (:parent #14))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #8))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #8) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #11) #("See " 0 4 (:parent #14)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #14)) #(".\n" 0 2 (:parent #14))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #9))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #9) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #12) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #15)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #15)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #15))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #10))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #13))) :mode section :granularity nil :parent #10) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #13) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #16) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #19)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #19) #("PATH" 0 4 (:parent #23))) #("and R" 0 5 (:parent #19)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #19) #("LIBS" 0 4 (:parent #25))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #19) #("SITE" 0 4 (:parent #26))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #19))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #16)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #16) #("On one system:\n" 0 15 (:parent #21))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #16)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #16) #("and perhaps a few more.\n" 0 24 (:parent #23))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #14)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #14) #("data" 0 4 (:parent #56))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #14)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #14) #("files" 0 5 (:parent #58))) #("/genotype'" 0 10 (:parent #14))) :mode nil :granularity nil :parent #10) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #14) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #17) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #20)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #20) #("data" 0 4 (:parent #24))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #20)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #20) #("settings.py" 0 11 (:parent #26))) #("(see above in\nthis document).\n" 0 30 (:parent #20))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #17) #("You can use the GENENETWORK" 0 27 (:parent #21)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #21) #("FILES" 0 5 (:parent #25))) #("switch to set the datadir, for example\n" 0 39 (:parent #21))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #17)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #15))) :mode nil :granularity nil :parent #10) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #15) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #18) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #21))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #16))) :mode nil :granularity nil :parent #10) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #16) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #19) #("This error\n" 0 11 (:parent #22))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #19)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #19) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #24))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #19) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #25)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #25) #("LIBS" 0 4 (:parent #29))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #25) #("SITE" 0 4 (:parent #30))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #25))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #17))) :mode nil :granularity nil :parent #10) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #17) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #20) #("The following error\n" 0 20 (:parent #23))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #20)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #20) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #25))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #20)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #20) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #27))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #20)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #20) #("if that works run genenetwork after setting SQL" 0 47 (:parent #29)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #29) #("URI" 0 3 (:parent #33))) #("to something like\n" 0 18 (:parent #29))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #20))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #11))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #11) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #14) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #17))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #14) #("#+begin" 0 7 (:parent #18)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #18) #("src" 0 3 (:parent #22))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #18))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #14) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #19))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #14) #(" yes\n env GUIX" 0 30 (:parent #20)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #20) #("PACKAGE" 0 7 (:parent #24))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #20) #("PATH" 0 4 (:parent #25))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #20))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #14) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #21))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #14) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #22)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #22) #("PACKAGE" 0 7 (:parent #26))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #22) #("PATH" 0 4 (:parent #27))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #22))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #14) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #23))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #14) #(" which should have the same HASH values " 0 48 (:parent #24)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #24) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #28))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #24)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #24)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #24)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #34))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #35))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #24)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #24)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #39))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #40))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #24)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #42))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #43))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #24)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #24)))))) "") org-export-data((org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #0) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #3))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #4))) :mode nil :granularity nil :parent #0) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #4) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #7) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #13) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #16) #("Introduction" 0 12 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #14) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #17) #("Install" 0 7 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #15) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #18) #("Running GN2" 0 11 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #16) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #19) #("Run MariaDB server" 0 18 (:parent #22))) #("\n" 0 1 (:parent #19))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #16) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #23) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #26) #("Install MariaDB with GNU GUIx" 0 29 (:parent #29))) #("\n" 0 1 (:parent #26)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #20) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #24) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #27) #("Load the small database in MySQL" 0 32 (:parent #30))) #("\n" 0 1 (:parent #27)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #17) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #20) #("GN2 Dependency Graph" 0 20 (:parent #23))) #("\n" 0 1 (:parent #20)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #18) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #21) #("Working with the GN2 source code" 0 32 (:parent #24))) #("\n" 0 1 (:parent #21)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #19) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #22) #("Read more" 0 9 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #20) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #23) #("Trouble shooting" 0 16 (:parent #26))) #("\n" 0 1 (:parent #23))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #20) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #27) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #30) #("ImportError: No module named jinja2" 0 35 (:parent #33))) #("\n" 0 1 (:parent #30)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #28) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #31) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #34)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #34) #("data" 0 4 (:parent #38))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #34)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #34) #("files" 0 5 (:parent #40))) #("/genotype'" 0 10 (:parent #34))) #("\n" 0 1 (:parent #31)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #29) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #32) #("Can't run a module" 0 18 (:parent #35))) #("\n" 0 1 (:parent #32)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #30) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #33) #("Rpy2 error 'show' now found" 0 27 (:parent #36))) #("\n" 0 1 (:parent #33)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #31) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #34) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #37))) #("\n" 0 1 (:parent #34)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #21) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #24) #("IRC session" 0 11 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #10) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #22) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #25) #("NOTES" 0 5 (:parent #28))) #("\n" 0 1 (:parent #25))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #22) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #26) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #29) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #32) #("Deploying GN2 official" 0 22 (:parent #35))) #("\n" 0 1 (:parent #32))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #5))) :mode nil :granularity nil :parent #0) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #5) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #8) #("Large system deployments can get very " 0 38 (:parent #11)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #11) #("complex" 0 7 (:parent #15))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #11)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #11) #("Guix-notes" 0 10 (:parent #17))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #11))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #8) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #12) #("Guix bioinformatics" 0 19 (:parent #16))) #("and " 0 4 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #12) #("GNU Guix" 0 8 (:parent #18))) #(".\n" 0 2 (:parent #12))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #8) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #13)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #13) #("GN2 Dependency Graph" 0 20 (:parent #17))) #(".\n" 0 2 (:parent #13))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #6))) :mode nil :granularity nil :parent #0) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #6) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #9) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #12)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #12)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #12))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #7))) :mode nil :granularity nil :parent #0) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #7) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #10) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #13)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #13) #("default" 0 7 (:parent #17)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #17) #("settings.py" 0 11 (:parent #21)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #13))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #10)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #10) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #15))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #10)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #10) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #17))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #8))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #11))) :mode section :granularity nil :parent #8) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #11) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #14) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #17) #("Note: we moved to MariaDB" 0 25 (:parent #20))) #("\n" 0 1 (:parent #17))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #14) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #18))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #14) #("As root configure and run\n" 0 26 (:parent #19))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #14) #("If you want to run as root you may have to set\n" 0 47 (:parent #21))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #14) #("You also need to set\n" 0 21 (:parent #23))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #14) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #25))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #14) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #26))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #14) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #28))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #14) #("When you get errors like:\n" 0 26 (:parent #30))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #14) #("you may need to set\n" 0 20 (:parent #32))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #14)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #12))) :mode nil :granularity nil :parent #8) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #12) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #15) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #18)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #18) #("webqtl" 0 6 (:parent #22))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #18) #("s" 0 1 (:parent #23))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #18)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #18) #("webqtl" 0 6 (:parent #25))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #18) #("plant" 0 5 (:parent #26))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #18))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #15) #("Download one database from\n" 0 27 (:parent #19))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #15) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #20)) #("\n" 0 1 (:parent #20))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #15) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #21)) #("\n" 0 1 (:parent #21))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #15) #("Check the md5sum.\n" 0 18 (:parent #22))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #15) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #23))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #15)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #15) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #25))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #15)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #15) #("and\n" 0 4 (:parent #27))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #15) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #29))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #15) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #31))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #15) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #32))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #15) #("Note for the plant database you can rename it to db" 0 51 (:parent #33)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #33) #("webqtl" 0 6 (:parent #37))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #33) #("s" 0 1 (:parent #38))) #(", or\nchange the settings in etc/default" 0 39 (:parent #33)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #33) #("settings.py" 0 11 (:parent #40))) #("to match your path.\n" 0 20 (:parent #33)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #9))) :mode nil :granularity nil :parent #0) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #9) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #12) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #15))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #12) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #16)) #("\n" 0 1 (:parent #16))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #10))) :mode nil :granularity nil :parent #0) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #10) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #13) #("See " 0 4 (:parent #16)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #16)) #(".\n" 0 2 (:parent #16))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #11))) :mode nil :granularity nil :parent #0) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #11) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #14) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #17)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #17))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #12))) :mode nil :granularity nil :parent #0) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #15))) :mode section :granularity nil :parent #12) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #15) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #18) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #21)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #21) #("PATH" 0 4 (:parent #25))) #("and R" 0 5 (:parent #21)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #21) #("LIBS" 0 4 (:parent #27))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #21) #("SITE" 0 4 (:parent #28))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #21))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #18)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #18) #("On one system:\n" 0 15 (:parent #23))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #18)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #18) #("and perhaps a few more.\n" 0 24 (:parent #25))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #16)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #16) #("data" 0 4 (:parent #58))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #16)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #16) #("files" 0 5 (:parent #60))) #("/genotype'" 0 10 (:parent #16))) :mode nil :granularity nil :parent #12) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #16) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #19) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #22)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #22) #("data" 0 4 (:parent #26))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #22)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #22) #("settings.py" 0 11 (:parent #28))) #("(see above in\nthis document).\n" 0 30 (:parent #22))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #19) #("You can use the GENENETWORK" 0 27 (:parent #23)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #23) #("FILES" 0 5 (:parent #27))) #("switch to set the datadir, for example\n" 0 39 (:parent #23))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #19)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #17))) :mode nil :granularity nil :parent #12) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #17) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #20) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #23))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #18))) :mode nil :granularity nil :parent #12) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #18) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #21) #("This error\n" 0 11 (:parent #24))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #21)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #21) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #26))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #21) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #27)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #27) #("LIBS" 0 4 (:parent #31))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #27) #("SITE" 0 4 (:parent #32))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #27))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #19))) :mode nil :granularity nil :parent #12) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #19) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #22) #("The following error\n" 0 20 (:parent #25))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #22)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #22) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #27))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #22)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #22) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #29))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #22)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #22) #("if that works run genenetwork after setting SQL" 0 47 (:parent #31)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #31) #("URI" 0 3 (:parent #35))) #("to something like\n" 0 18 (:parent #31))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #22))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #13))) :mode nil :granularity nil :parent #0) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #13) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #16) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #19))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #16) #("#+begin" 0 7 (:parent #20)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #20) #("src" 0 3 (:parent #24))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #20))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #16) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #21))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #16) #(" yes\n env GUIX" 0 30 (:parent #22)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #22) #("PACKAGE" 0 7 (:parent #26))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #22) #("PATH" 0 4 (:parent #27))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #22))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #16) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #23))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #16) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #24)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #24) #("PACKAGE" 0 7 (:parent #28))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #24) #("PATH" 0 4 (:parent #29))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #24))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #16) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #25))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #16) #(" which should have the same HASH values " 0 48 (:parent #26)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #26) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #30))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #26)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #26)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #26)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #36))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #37))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #26)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #26)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #41))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #42))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #26)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #26) #("PACKAGE" 0 7 (:parent #44))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #26) #("PATH" 0 4 (:parent #45))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #26)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #26)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #26)))))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section "
\n

%s:

\n
\n%s\n
\n
" :html-format-drawer-function #f(compiled-function (name contents) #) :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "
\n UP \n |\n HOME \n
" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "

Author: %a (%e)

\n

Date: %d

\n

%c

\n

%v

")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("" . "") :html-table-header-tags ("" . "") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (italic . "%s") (strike-through . "%s") (underline . "%s") (verbatim . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "" :html-table-row-close-tag "" :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 29.4 (Org mode 9.6.15)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services" 0 31 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:begin 1 :contents-begin 1 :contents-end 15495 :end 15495 :robust-begin 3 :robust-end 15493 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #338) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #341))) (headline (:raw-value "Table of Contents" :begin 43 :end 1231 :pre-blank 0 :contents-begin 121 :contents-end 1230 :robust-begin 123 :robust-end 1228 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #342))) :mode nil :granularity nil :parent #338) (section (:begin 121 :end 1231 :contents-begin 121 :contents-end 1230 :robust-begin 121 :robust-end 1228 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent #342) (plain-list (:type unordered :begin 121 :end 1230 :contents-begin 121 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent #345) (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 124 :end 156 :contents-begin 124 :contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent #351) (link (:type "custom-id" :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil :begin 124 :end 155 :contents-begin 141 :contents-end 153 :post-blank 0 :parent #354) #("Introduction" 0 12 (:parent #357))) #("\n" 0 1 (:parent #354)))) (item (:bullet "- " :begin 156 :end 181 :contents-begin 159 :contents-end 181 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 :post-blank 0 :post-affiliated 159 :mode nil :granularity nil :parent #352) (link (:type "custom-id" :path "install" :format bracket :raw-link "#install" :application nil :search-option nil :begin 159 :end 180 :contents-begin 171 :contents-end 178 :post-blank 0 :parent #355) #("Install" 0 7 (:parent #358))) #("\n" 0 1 (:parent #355)))) (item (:bullet "- " :begin 181 :end 214 :contents-begin 184 :contents-end 214 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 181 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 184 :end 214 :contents-begin 184 :contents-end 214 :post-blank 0 :post-affiliated 184 :mode nil :granularity nil :parent #353) (link (:type "custom-id" :path "running-gn2" :format bracket :raw-link "#running-gn2" :application nil :search-option nil :begin 184 :end 213 :contents-begin 200 :contents-end 211 :post-blank 0 :parent #356) #("Running GN2" 0 11 (:parent #359))) #("\n" 0 1 (:parent #356)))) (item (:bullet "- " :begin 214 :end 409 :contents-begin 217 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 214 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 217 :end 261 :contents-begin 217 :contents-end 261 :post-blank 0 :post-affiliated 217 :mode nil :granularity nil :parent #354) (link (:type "custom-id" :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil :begin 217 :end 260 :contents-begin 240 :contents-end 258 :post-blank 0 :parent #357) #("Run MariaDB server" 0 18 (:parent #360))) #("\n" 0 1 (:parent #357))) (plain-list (:type unordered :begin 261 :end 409 :contents-begin 261 :contents-end 409 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 261 :mode nil :granularity nil :parent #354) (item (:bullet "- " :begin 261 :end 332 :contents-begin 266 :contents-end 332 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 261 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 266 :end 332 :contents-begin 266 :contents-end 332 :post-blank 0 :post-affiliated 266 :mode nil :granularity nil :parent #361) (link (:type "custom-id" :path "install-mariadb-with-gnu-guix" :format bracket :raw-link "#install-mariadb-with-gnu-guix" :application nil :search-option nil :begin 266 :end 331 :contents-begin 300 :contents-end 329 :post-blank 0 :parent #364) #("Install MariaDB with GNU GUIx" 0 29 (:parent #367))) #("\n" 0 1 (:parent #364)))) (item (:bullet "- " :begin 332 :end 409 :contents-begin 337 :contents-end 409 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 332 :tag nil :mode item :granularity nil :parent #358) (paragraph (:begin 337 :end 409 :contents-begin 337 :contents-end 409 :post-blank 0 :post-affiliated 337 :mode nil :granularity nil :parent #362) (link (:type "custom-id" :path "load-the-small-database-in-mysql" :format bracket :raw-link "#load-the-small-database-in-mysql" :application nil :search-option nil :begin 337 :end 408 :contents-begin 374 :contents-end 406 :post-blank 0 :parent #365) #("Load the small database in MySQL" 0 32 (:parent #368))) #("\n" 0 1 (:parent #365)))))) (item (:bullet "- " :begin 409 :end 460 :contents-begin 412 :contents-end 460 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 409 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 412 :end 460 :contents-begin 412 :contents-end 460 :post-blank 0 :post-affiliated 412 :mode nil :granularity nil :parent #355) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 412 :end 459 :contents-begin 437 :contents-end 457 :post-blank 0 :parent #358) #("GN2 Dependency Graph" 0 20 (:parent #361))) #("\n" 0 1 (:parent #358)))) (item (:bullet "- " :begin 460 :end 535 :contents-begin 463 :contents-end 535 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 460 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 463 :end 535 :contents-begin 463 :contents-end 535 :post-blank 0 :post-affiliated 463 :mode nil :granularity nil :parent #356) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 463 :end 534 :contents-begin 500 :contents-end 532 :post-blank 0 :parent #359) #("Working with the GN2 source code" 0 32 (:parent #362))) #("\n" 0 1 (:parent #359)))) (item (:bullet "- " :begin 535 :end 564 :contents-begin 538 :contents-end 564 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 535 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 538 :end 564 :contents-begin 538 :contents-end 564 :post-blank 0 :post-affiliated 538 :mode nil :granularity nil :parent #357) (link (:type "custom-id" :path "read-more" :format bracket :raw-link "#read-more" :application nil :search-option nil :begin 538 :end 563 :contents-begin 552 :contents-end 561 :post-blank 0 :parent #360) #("Read more" 0 9 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:bullet "- " :begin 564 :end 1119 :contents-begin 567 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 564 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 567 :end 607 :contents-begin 567 :contents-end 607 :post-blank 0 :post-affiliated 567 :mode nil :granularity nil :parent #358) (link (:type "custom-id" :path "trouble-shooting" :format bracket :raw-link "#trouble-shooting" :application nil :search-option nil :begin 567 :end 606 :contents-begin 588 :contents-end 604 :post-blank 0 :parent #361) #("Trouble shooting" 0 16 (:parent #364))) #("\n" 0 1 (:parent #361))) (plain-list (:type unordered :begin 607 :end 1119 :contents-begin 607 :contents-end 1119 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 607 :mode nil :granularity nil :parent #358) (item (:bullet "- " :begin 607 :end 689 :contents-begin 612 :contents-end 689 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 607 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 612 :end 689 :contents-begin 612 :contents-end 689 :post-blank 0 :post-affiliated 612 :mode nil :granularity nil :parent #365) (link (:type "custom-id" :path "importerror-no-module-named-jinja2" :format bracket :raw-link "#importerror-no-module-named-jinja2" :application nil :search-option nil :begin 612 :end 688 :contents-begin 651 :contents-end 686 :post-blank 0 :parent #368) #("ImportError: No module named jinja2" 0 35 (:parent #371))) #("\n" 0 1 (:parent #368)))) (item (:bullet "- " :begin 689 :end 900 :contents-begin 694 :contents-end 900 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 689 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 694 :end 900 :contents-begin 694 :contents-end 900 :post-blank 0 :post-affiliated 694 :mode nil :granularity nil :parent #366) (link (:type "custom-id" :path "error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :format bracket :raw-link "#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype" :application nil :search-option nil :begin 694 :end 899 :contents-begin 793 :contents-end 897 :post-blank 0 :parent #369) #("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #372)) (subscript (:begin 833 :end 838 :use-brackets-p nil :contents-begin 834 :contents-end 838 :post-blank 0 :parent #372) #("data" 0 4 (:parent #376))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #372)) (subscript (:begin 881 :end 887 :use-brackets-p nil :contents-begin 882 :contents-end 887 :post-blank 0 :parent #372) #("files" 0 5 (:parent #378))) #("/genotype'" 0 10 (:parent #372))) #("\n" 0 1 (:parent #369)))) (item (:bullet "- " :begin 900 :end 948 :contents-begin 905 :contents-end 948 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 900 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 905 :end 948 :contents-begin 905 :contents-end 948 :post-blank 0 :post-affiliated 905 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "cant-run-a-module" :format bracket :raw-link "#cant-run-a-module" :application nil :search-option nil :begin 905 :end 947 :contents-begin 927 :contents-end 945 :post-blank 0 :parent #370) #("Can't run a module" 0 18 (:parent #373))) #("\n" 0 1 (:parent #370)))) (item (:bullet "- " :begin 948 :end 1013 :contents-begin 953 :contents-end 1013 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 948 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 953 :end 1013 :contents-begin 953 :contents-end 1013 :post-blank 0 :post-affiliated 953 :mode nil :granularity nil :parent #368) (link (:type "custom-id" :path "rpy2-error-show-now-found" :format bracket :raw-link "#rpy2-error-show-now-found" :application nil :search-option nil :begin 953 :end 1012 :contents-begin 983 :contents-end 1010 :post-blank 0 :parent #371) #("Rpy2 error 'show' now found" 0 27 (:parent #374))) #("\n" 0 1 (:parent #371)))) (item (:bullet "- " :begin 1013 :end 1119 :contents-begin 1018 :contents-end 1119 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1013 :tag nil :mode item :granularity nil :parent #362) (paragraph (:begin 1018 :end 1119 :contents-begin 1018 :contents-end 1119 :post-blank 0 :post-affiliated 1018 :mode nil :granularity nil :parent #369) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 1018 :end 1118 :contents-begin 1069 :contents-end 1116 :post-blank 0 :parent #372) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #375))) #("\n" 0 1 (:parent #372)))))) (item (:bullet "- " :begin 1119 :end 1152 :contents-begin 1122 :contents-end 1152 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1119 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1122 :end 1152 :contents-begin 1122 :contents-end 1152 :post-blank 0 :post-affiliated 1122 :mode nil :granularity nil :parent #359) (link (:type "custom-id" :path "irc-session" :format bracket :raw-link "#irc-session" :application nil :search-option nil :begin 1122 :end 1151 :contents-begin 1138 :contents-end 1149 :post-blank 0 :parent #362) #("IRC session" 0 11 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:bullet "- " :begin 1152 :end 1230 :contents-begin 1155 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1152 :tag nil :mode item :granularity nil :parent #348) (paragraph (:begin 1155 :end 1173 :contents-begin 1155 :contents-end 1173 :post-blank 0 :post-affiliated 1155 :mode nil :granularity nil :parent #360) (link (:type "custom-id" :path "notes" :format bracket :raw-link "#notes" :application nil :search-option nil :begin 1155 :end 1172 :contents-begin 1165 :contents-end 1170 :post-blank 0 :parent #363) #("NOTES" 0 5 (:parent #366))) #("\n" 0 1 (:parent #363))) (plain-list (:type unordered :begin 1173 :end 1230 :contents-begin 1173 :contents-end 1230 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :post-blank 0 :post-affiliated 1173 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 1173 :end 1230 :contents-begin 1178 :contents-end 1230 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 409) (261 3 "- " nil nil nil 332) (332 3 "- " nil nil nil 409) (409 1 "- " nil nil nil 460) (460 1 "- " nil nil nil 535) (535 1 "- " nil nil nil 564) (564 1 "- " nil nil nil 1119) (607 3 "- " nil nil nil 689) (689 3 "- " nil nil nil 900) (900 3 "- " nil nil nil 948) (948 3 "- " nil nil nil 1013) (1013 3 "- " nil nil nil 1119) (1119 1 "- " nil nil nil 1152) (1152 1 "- " nil nil nil 1230) (1173 3 "- " nil nil nil 1230)) :pre-blank 0 :post-blank 0 :post-affiliated 1173 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 1178 :end 1230 :contents-begin 1178 :contents-end 1230 :post-blank 0 :post-affiliated 1178 :mode nil :granularity nil :parent #367) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1178 :end 1229 :contents-begin 1205 :contents-end 1227 :post-blank 0 :parent #370) #("Deploying GN2 official" 0 22 (:parent #373))) #("\n" 0 1 (:parent #370))))))))) (headline (:raw-value "Introduction" :begin 1231 :end 2119 :pre-blank 1 :contents-begin 1247 :contents-end 2118 :robust-begin 1249 :robust-end 2116 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1231 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1247 :end 2119 :contents-begin 1247 :contents-end 2118 :robust-begin 1247 :robust-end 2116 :post-blank 1 :post-affiliated 1247 :mode section :granularity nil :parent #343) (paragraph (:begin 1247 :end 1633 :contents-begin 1247 :contents-end 1632 :post-blank 1 :post-affiliated 1247 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1285 :end 1346 :contents-begin 1337 :contents-end 1344 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1476 :end 1550 :contents-begin 1538 :contents-end 1548 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1633 :end 1983 :contents-begin 1633 :contents-end 1982 :post-blank 1 :post-affiliated 1633 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1851 :end 1927 :contents-begin 1905 :contents-end 1924 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 1931 :end 1980 :contents-begin 1970 :contents-end 1978 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1983 :end 2118 :contents-begin 1983 :contents-end 2118 :post-blank 0 :post-affiliated 1983 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2069 :end 2116 :contents-begin 2094 :contents-end 2114 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2119 :end 2368 :pre-blank 1 :contents-begin 2130 :contents-end 2367 :robust-begin 2132 :robust-end 2365 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2119 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2130 :end 2368 :contents-begin 2130 :contents-end 2367 :robust-begin 2130 :robust-end 2365 :post-blank 1 :post-affiliated 2130 :mode section :granularity nil :parent #344) (paragraph (:begin 2130 :end 2367 :contents-begin 2130 :contents-end 2367 :post-blank 0 :post-affiliated 2130 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2247 :end 2285 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2368 :end 2849 :pre-blank 1 :contents-begin 2383 :contents-end 2848 :robust-begin 2385 :robust-end 2846 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2368 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2383 :end 2849 :contents-begin 2383 :contents-end 2848 :robust-begin 2383 :robust-end 2846 :post-blank 1 :post-affiliated 2383 :mode section :granularity nil :parent #345) (paragraph (:begin 2383 :end 2578 :contents-begin 2383 :contents-end 2577 :post-blank 1 :post-affiliated 2383 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2436 :end 2487 :contents-begin 2466 :contents-end 2485 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2473 :end 2485 :use-brackets-p nil :contents-begin 2474 :contents-end 2485 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2578 :end 2608 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2578 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2608 :end 2686 :contents-begin 2608 :contents-end 2685 :post-blank 1 :post-affiliated 2608 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2686 :end 2769 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2686 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2769 :end 2848 :contents-begin 2769 :contents-end 2848 :post-blank 0 :post-affiliated 2769 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 2849 :end 5700 :pre-blank 0 :contents-begin 2870 :contents-end 5699 :robust-begin 2872 :robust-end 5697 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2849 :title (#("Run MariaDB server" 0 18 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2870 :end 4168 :pre-blank 1 :contents-begin 2904 :contents-end 4167 :robust-begin 2906 :robust-end 4165 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2870 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 2904 :end 4168 :contents-begin 2904 :contents-end 4167 :robust-begin 2904 :robust-end 4165 :post-blank 1 :post-affiliated 2904 :mode section :granularity nil :parent #349) (paragraph (:begin 2904 :end 2933 :contents-begin 2904 :contents-end 2932 :post-blank 1 :post-affiliated 2904 :mode planning :granularity nil :parent #352) (italic (:begin 2904 :end 2931 :post-blank 0 :contents-begin 2905 :contents-end 2930 :parent #355) #("Note: we moved to MariaDB" 0 25 (:parent #358))) #("\n" 0 1 (:parent #355))) (paragraph (:begin 2933 :end 3070 :contents-begin 2933 :contents-end 3069 :post-blank 1 :post-affiliated 2933 :mode nil :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #356))) (paragraph (:begin 3070 :end 3097 :contents-begin 3070 :contents-end 3096 :post-blank 1 :post-affiliated 3070 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #357))) (src-block (:language "bash" :switches nil :parameters nil :begin 3097 :end 3393 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmysqld --datadir=/home/mariadb/database --initialize-insecure\nmkdir -p /var/run/mariadbd\nchown mariadb.mariadb /var/run/mariadbd\nmysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 3097 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3393 :end 3441 :contents-begin 3393 :contents-end 3440 :post-blank 1 :post-affiliated 3393 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #359))) (fixed-width (:begin 3441 :end 3481 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3441 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3481 :end 3503 :contents-begin 3481 :contents-end 3502 :post-blank 1 :post-affiliated 3481 :mode nil :granularity nil :parent #352) #("You also need to set\n" 0 21 (:parent #361))) (fixed-width (:begin 3503 :end 3526 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3503 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3526 :end 3606 :contents-begin 3526 :contents-end 3605 :post-blank 1 :post-affiliated 3526 :mode nil :granularity nil :parent #352) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #363))) (paragraph (:begin 3606 :end 3675 :contents-begin 3606 :contents-end 3674 :post-blank 1 :post-affiliated 3606 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #364))) (fixed-width (:begin 3675 :end 3790 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3675 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3790 :end 3868 :contents-begin 3790 :contents-end 3867 :post-blank 1 :post-affiliated 3790 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #366))) (fixed-width (:begin 3868 :end 3978 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3868 :mode nil :granularity nil :parent #352)) (paragraph (:begin 3978 :end 4005 :contents-begin 3978 :contents-end 4004 :post-blank 1 :post-affiliated 3978 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #368))) (fixed-width (:begin 4005 :end 4119 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4005 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4119 :end 4140 :contents-begin 4119 :contents-end 4139 :post-blank 1 :post-affiliated 4119 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #370))) (fixed-width (:begin 4140 :end 4167 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4140 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 4168 :end 5700 :pre-blank 1 :contents-begin 4205 :contents-end 5699 :robust-begin 4207 :robust-end 5697 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4168 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4205 :end 5700 :contents-begin 4205 :contents-end 5699 :robust-begin 4205 :robust-end 5697 :post-blank 1 :post-affiliated 4205 :mode section :granularity nil :parent #350) (paragraph (:begin 4205 :end 4512 :contents-begin 4205 :contents-end 4511 :post-blank 1 :post-affiliated 4205 :mode planning :granularity nil :parent #353) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #356)) (subscript (:begin 4368 :end 4375 :use-brackets-p nil :contents-begin 4369 :contents-end 4375 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4375 :end 4377 :use-brackets-p nil :contents-begin 4376 :contents-end 4377 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4453 :end 4460 :use-brackets-p nil :contents-begin 4454 :contents-end 4460 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4460 :end 4466 :use-brackets-p nil :contents-begin 4461 :contents-end 4466 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4512 :end 4540 :contents-begin 4512 :contents-end 4539 :post-blank 1 :post-affiliated 4512 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4540 :end 4588 :contents-begin 4540 :contents-end 4587 :post-blank 1 :post-affiliated 4540 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4540 :end 4586 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4588 :end 4647 :contents-begin 4588 :contents-end 4646 :post-blank 1 :post-affiliated 4588 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4588 :end 4645 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4647 :end 4666 :contents-begin 4647 :contents-end 4665 :post-blank 1 :post-affiliated 4647 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4666 :end 4737 :contents-begin 4666 :contents-end 4736 :post-blank 1 :post-affiliated 4666 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4737 :end 4838 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4737 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4838 :end 4885 :contents-begin 4838 :contents-end 4884 :post-blank 1 :post-affiliated 4838 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 4885 :end 4902 :value "myslq -u root" :post-blank 2 :post-affiliated 4885 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4902 :end 4907 :contents-begin 4902 :contents-end 4906 :post-blank 1 :post-affiliated 4902 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 4907 :end 5133 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 4907 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5133 :end 5198 :contents-begin 5133 :contents-end 5197 :post-blank 1 :post-affiliated 5133 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5198 :end 5297 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5198 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5297 :end 5404 :contents-begin 5297 :contents-end 5403 :post-blank 1 :post-affiliated 5297 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5404 :end 5567 :contents-begin 5404 :contents-end 5566 :post-blank 1 :post-affiliated 5404 :mode nil :granularity nil :parent #353) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #370))) (paragraph (:begin 5567 :end 5699 :contents-begin 5567 :contents-end 5699 :post-blank 0 :post-affiliated 5567 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5618 :end 5625 :use-brackets-p nil :contents-begin 5619 :contents-end 5625 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5625 :end 5627 :use-brackets-p nil :contents-begin 5626 :contents-end 5627 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5666 :end 5679 :use-brackets-p nil :contents-begin 5667 :contents-end 5678 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5700 :end 5864 :pre-blank 1 :contents-begin 5724 :contents-end 5863 :robust-begin 5726 :robust-end 5861 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5700 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5724 :end 5864 :contents-begin 5724 :contents-end 5863 :robust-begin 5724 :robust-end 5861 :post-blank 1 :post-affiliated 5724 :mode section :granularity nil :parent #347) (paragraph (:begin 5724 :end 5785 :contents-begin 5724 :contents-end 5784 :post-blank 1 :post-affiliated 5724 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5785 :end 5863 :contents-begin 5815 :contents-end 5863 :post-blank 0 :post-affiliated 5815 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5815 :end 5862 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 5864 :end 5926 :pre-blank 1 :contents-begin 5900 :contents-end 5925 :robust-begin 5902 :robust-end 5923 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5864 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5900 :end 5926 :contents-begin 5900 :contents-end 5925 :robust-begin 5900 :robust-end 5923 :post-blank 1 :post-affiliated 5900 :mode section :granularity nil :parent #348) (paragraph (:begin 5900 :end 5925 :contents-begin 5900 :contents-end 5925 :post-blank 0 :post-affiliated 5900 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5904 :end 5923 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Read more" :begin 5926 :end 6076 :pre-blank 1 :contents-begin 5939 :contents-end 6075 :robust-begin 5941 :robust-end 6073 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5926 :title (#("Read more" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5939 :end 6076 :contents-begin 5939 :contents-end 6075 :robust-begin 5939 :robust-end 6073 :post-blank 1 :post-affiliated 5939 :mode section :granularity nil :parent #349) (paragraph (:begin 5939 :end 6075 :contents-begin 5939 :contents-end 6075 :post-blank 0 :post-affiliated 5939 :mode planning :granularity nil :parent #352) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #355)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 5994 :end 6014 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #355))))) (headline (:raw-value "Trouble shooting" :begin 6076 :end 8527 :pre-blank 1 :contents-begin 6096 :contents-end 8525 :robust-begin 6098 :robust-end 8523 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6076 :title (#("Trouble shooting" 0 16 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6096 :end 6630 :pre-blank 1 :contents-begin 6136 :contents-end 6630 :robust-begin 6138 :robust-end 6628 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6096 :title (#("ImportError: No module named jinja2" 0 35 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6136 :end 6630 :contents-begin 6136 :contents-end 6630 :robust-begin 6136 :robust-end 6628 :post-blank 0 :post-affiliated 6136 :mode section :granularity nil :parent #353) (paragraph (:begin 6136 :end 6371 :contents-begin 6136 :contents-end 6370 :post-blank 1 :post-affiliated 6136 :mode planning :granularity nil :parent #356) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #359)) (subscript (:begin 6303 :end 6309 :use-brackets-p nil :contents-begin 6304 :contents-end 6308 :post-blank 1 :parent #359) #("PATH" 0 4 (:parent #363))) #("and R" 0 5 (:parent #359)) (subscript (:begin 6314 :end 6319 :use-brackets-p nil :contents-begin 6315 :contents-end 6319 :post-blank 0 :parent #359) #("LIBS" 0 4 (:parent #365))) (subscript (:begin 6319 :end 6325 :use-brackets-p nil :contents-begin 6320 :contents-end 6324 :post-blank 1 :parent #359) #("SITE" 0 4 (:parent #366))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #359))) (fixed-width (:begin 6371 :end 6402 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6371 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6402 :end 6418 :contents-begin 6402 :contents-end 6417 :post-blank 1 :post-affiliated 6402 :mode nil :granularity nil :parent #356) #("On one system:\n" 0 15 (:parent #361))) (fixed-width (:begin 6418 :end 6606 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6418 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6606 :end 6630 :contents-begin 6606 :contents-end 6630 :post-blank 0 :post-affiliated 6606 :mode nil :granularity nil :parent #356) #("and perhaps a few more.\n" 0 24 (:parent #363))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6630 :end 7126 :pre-blank 1 :contents-begin 6739 :contents-end 7125 :robust-begin 6741 :robust-end 7123 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6630 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #354)) (subscript (:begin 6673 :end 6678 :use-brackets-p nil :contents-begin 6674 :contents-end 6678 :post-blank 0 :parent #354) #("data" 0 4 (:parent #396))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #354)) (subscript (:begin 6721 :end 6727 :use-brackets-p nil :contents-begin 6722 :contents-end 6727 :post-blank 0 :parent #354) #("files" 0 5 (:parent #398))) #("/genotype'" 0 10 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 6739 :end 7126 :contents-begin 6739 :contents-end 7125 :robust-begin 6739 :robust-end 7123 :post-blank 1 :post-affiliated 6739 :mode section :granularity nil :parent #354) (paragraph (:begin 6739 :end 6961 :contents-begin 6739 :contents-end 6960 :post-blank 1 :post-affiliated 6739 :mode planning :granularity nil :parent #357) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #360)) (subscript (:begin 6788 :end 6793 :use-brackets-p nil :contents-begin 6789 :contents-end 6793 :post-blank 0 :parent #360) #("data" 0 4 (:parent #364))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #360)) (subscript (:begin 6917 :end 6930 :use-brackets-p nil :contents-begin 6918 :contents-end 6929 :post-blank 1 :parent #360) #("settings.py" 0 11 (:parent #366))) #("(see above in\nthis document).\n" 0 30 (:parent #360))) (paragraph (:begin 6961 :end 7035 :contents-begin 6961 :contents-end 7034 :post-blank 1 :post-affiliated 6961 :mode nil :granularity nil :parent #357) #("You can use the GENENETWORK" 0 27 (:parent #361)) (subscript (:begin 6988 :end 6995 :use-brackets-p nil :contents-begin 6989 :contents-end 6994 :post-blank 1 :parent #361) #("FILES" 0 5 (:parent #365))) #("switch to set the datadir, for example\n" 0 39 (:parent #361))) (fixed-width (:begin 7035 :end 7125 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7035 :mode nil :granularity nil :parent #357)))) (headline (:raw-value "Can't run a module" :begin 7126 :end 7360 :pre-blank 1 :contents-begin 7149 :contents-end 7360 :robust-begin 7151 :robust-end 7358 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7126 :title (#("Can't run a module" 0 18 (:parent #355))) :mode nil :granularity nil :parent #350) (section (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :robust-begin 7149 :robust-end 7358 :post-blank 0 :post-affiliated 7149 :mode section :granularity nil :parent #355) (paragraph (:begin 7149 :end 7360 :contents-begin 7149 :contents-end 7360 :post-blank 0 :post-affiliated 7149 :mode planning :granularity nil :parent #358) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #361))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7360 :end 7861 :pre-blank 1 :contents-begin 7392 :contents-end 7860 :robust-begin 7394 :robust-end 7858 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7360 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #356))) :mode nil :granularity nil :parent #350) (section (:begin 7392 :end 7861 :contents-begin 7392 :contents-end 7860 :robust-begin 7392 :robust-end 7858 :post-blank 1 :post-affiliated 7392 :mode section :granularity nil :parent #356) (paragraph (:begin 7392 :end 7404 :contents-begin 7392 :contents-end 7403 :post-blank 1 :post-affiliated 7392 :mode planning :granularity nil :parent #359) #("This error\n" 0 11 (:parent #362))) (fixed-width (:begin 7404 :end 7484 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7404 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7484 :end 7615 :contents-begin 7484 :contents-end 7614 :post-blank 1 :post-affiliated 7484 :mode nil :granularity nil :parent #359) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #364))) (paragraph (:begin 7615 :end 7860 :contents-begin 7615 :contents-end 7860 :post-blank 0 :post-affiliated 7615 :mode nil :granularity nil :parent #359) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #365)) (subscript (:begin 7678 :end 7683 :use-brackets-p nil :contents-begin 7679 :contents-end 7683 :post-blank 0 :parent #365) #("LIBS" 0 4 (:parent #369))) (subscript (:begin 7683 :end 7688 :use-brackets-p nil :contents-begin 7684 :contents-end 7688 :post-blank 0 :parent #365) #("SITE" 0 4 (:parent #370))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #365))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7861 :end 8527 :pre-blank 1 :contents-begin 7913 :contents-end 8525 :robust-begin 7915 :robust-end 8523 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7861 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #357))) :mode nil :granularity nil :parent #350) (section (:begin 7913 :end 8527 :contents-begin 7913 :contents-end 8525 :robust-begin 7913 :robust-end 8523 :post-blank 2 :post-affiliated 7913 :mode section :granularity nil :parent #357) (paragraph (:begin 7913 :end 7934 :contents-begin 7913 :contents-end 7933 :post-blank 1 :post-affiliated 7913 :mode planning :granularity nil :parent #360) #("The following error\n" 0 20 (:parent #363))) (fixed-width (:begin 7934 :end 8129 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 7934 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8129 :end 8287 :contents-begin 8129 :contents-end 8286 :post-blank 1 :post-affiliated 8129 :mode nil :granularity nil :parent #360) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #365))) (fixed-width (:begin 8287 :end 8309 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8287 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8309 :end 8366 :contents-begin 8309 :contents-end 8365 :post-blank 1 :post-affiliated 8309 :mode nil :granularity nil :parent #360) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #367))) (fixed-width (:begin 8366 :end 8388 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8366 :mode nil :granularity nil :parent #360)) (paragraph (:begin 8388 :end 8459 :contents-begin 8388 :contents-end 8458 :post-blank 1 :post-affiliated 8388 :mode nil :granularity nil :parent #360) #("if that works run genenetwork after setting SQL" 0 47 (:parent #369)) (subscript (:begin 8435 :end 8440 :use-brackets-p nil :contents-begin 8436 :contents-end 8439 :post-blank 1 :parent #369) #("URI" 0 3 (:parent #373))) #("to something like\n" 0 18 (:parent #369))) (fixed-width (:begin 8459 :end 8525 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8459 :mode nil :granularity nil :parent #360))))) (headline (:raw-value "IRC session" :begin 8527 :end 15495 :pre-blank 1 :contents-begin 8542 :contents-end 15495 :robust-begin 8544 :robust-end 15493 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8527 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8542 :end 15495 :contents-begin 8542 :contents-end 15495 :robust-begin 8542 :robust-end 15493 :post-blank 0 :post-affiliated 8542 :mode section :granularity nil :parent #351) (paragraph (:begin 8542 :end 8651 :contents-begin 8542 :contents-end 8650 :post-blank 1 :post-affiliated 8542 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8651 :end 9212 :contents-begin 8651 :contents-end 9211 :post-blank 1 :post-affiliated 8651 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8658 :end 8662 :use-brackets-p nil :contents-begin 8659 :contents-end 8662 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9212 :end 9302 :contents-begin 9212 :contents-end 9301 :post-blank 1 :post-affiliated 9212 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9302 :end 9447 :contents-begin 9302 :contents-end 9446 :post-blank 1 :post-affiliated 9302 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9332 :end 9340 :use-brackets-p nil :contents-begin 9333 :contents-end 9340 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9340 :end 9345 :use-brackets-p nil :contents-begin 9341 :contents-end 9345 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9447 :end 9743 :contents-begin 9447 :contents-end 9742 :post-blank 1 :post-affiliated 9447 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9743 :end 10936 :contents-begin 9743 :contents-end 10935 :post-blank 1 :post-affiliated 9743 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10496 :end 10504 :use-brackets-p nil :contents-begin 10497 :contents-end 10504 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10504 :end 10509 :use-brackets-p nil :contents-begin 10505 :contents-end 10509 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10936 :end 11140 :contents-begin 10936 :contents-end 11139 :post-blank 1 :post-affiliated 10936 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11140 :end 15495 :contents-begin 11140 :contents-end 15495 :post-blank 0 :post-affiliated 11140 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11188 :end 12097 :post-blank 0 :contents-begin 11189 :contents-end 12096 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12897 :end 12962 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13210 :end 13243 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13467 :end 13475 :use-brackets-p nil :contents-begin 13468 :contents-end 13475 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13475 :end 13480 :use-brackets-p nil :contents-begin 13476 :contents-end 13480 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13596 :end 13623 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14193 :end 14201 :use-brackets-p nil :contents-begin 14194 :contents-end 14201 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14201 :end 14206 :use-brackets-p nil :contents-begin 14202 :contents-end 14206 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14865 :end 14873 :use-brackets-p nil :contents-begin 14866 :contents-end 14873 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14873 :end 14878 :use-brackets-p nil :contents-begin 14874 :contents-end 14878 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14992 :end 15024 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n [08:05]\n" 0 471 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) org-export-as(html nil nil t nil) org-export-to-buffer(html "*Org HTML Export*" nil nil nil t nil #f(compiled-function () #)) org-html-export-as-html(nil nil nil t) (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (let ((temp-buffer (generate-new-buffer " *temp*" t))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))))) eval-buffer(# nil "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t) #f(compiled-function (buffer file) #)(# "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") load-with-code-conversion("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t #f(compiled-function (buffer file) #)) command-line--load-script("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") command-line-1(("-scriptload" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el")) command-line() normal-top-level()
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 23:48:42 +0000