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")
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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 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: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 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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
\n
" :html-format-drawer-function #f(compiled-function (name contents) #%s:
\n\n%s\n
\nDate: %d
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