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 "Running Redis" :begin 2849 :end 2931 :pre-blank 1 :contents-begin 2866 :contents-end 2930 :robust-begin 2868 :robust-end 2928 :level 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 (#("Running Redis" 0 13 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2866 :end 2931 :contents-begin 2866 :contents-end 2930 :robust-begin 2866 :robust-end 2928 :post-blank 1 :post-affiliated 2866 :mode section :granularity nil :parent #180) (paragraph (:begin 2866 :end 2913 :contents-begin 2866 :contents-end 2912 :post-blank 1 :post-affiliated 2866 :mode planning :granularity nil :parent #183) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #186))) (fixed-width (:begin 2913 :end 2930 :value "appendonly yes" :post-blank 1 :post-affiliated 2913 :mode nil :granularity nil :parent #183)))) (headline (:raw-value "Run MariaDB server" :begin 2931 :end 5782 :pre-blank 0 :contents-begin 2952 :contents-end 5781 :robust-begin 2954 :robust-end 5779 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2931 :title (#("Run MariaDB server" 0 18 (:parent #181))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2952 :end 4250 :pre-blank 1 :contents-begin 2986 :contents-end 4249 :robust-begin 2988 :robust-end 4247 :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 2952 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #184))) :mode section :granularity nil :parent #181) (section (:begin 2986 :end 4250 :contents-begin 2986 :contents-end 4249 :robust-begin 2986 :robust-end 4247 :post-blank 1 :post-affiliated 2986 :mode section :granularity nil :parent #184) (paragraph (:begin 2986 :end 3015 :contents-begin 2986 :contents-end 3014 :post-blank 1 :post-affiliated 2986 :mode planning :granularity nil :parent #187) (italic (:begin 2986 :end 3013 :post-blank 0 :contents-begin 2987 :contents-end 3012 :parent #190) #("Note: we moved to MariaDB" 0 25 (:parent #193))) #("\n" 0 1 (:parent #190))) (paragraph (:begin 3015 :end 3152 :contents-begin 3015 :contents-end 3151 :post-blank 1 :post-affiliated 3015 :mode nil :granularity nil :parent #187) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #191))) (paragraph (:begin 3152 :end 3179 :contents-begin 3152 :contents-end 3178 :post-blank 1 :post-affiliated 3152 :mode nil :granularity nil :parent #187) #("As root configure and run\n" 0 26 (:parent #192))) (src-block (:language "bash" :switches nil :parameters nil :begin 3179 :end 3475 :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 3179 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3475 :end 3523 :contents-begin 3475 :contents-end 3522 :post-blank 1 :post-affiliated 3475 :mode nil :granularity nil :parent #187) #("If you want to run as root you may have to set\n" 0 47 (:parent #194))) (fixed-width (:begin 3523 :end 3563 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3523 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3563 :end 3585 :contents-begin 3563 :contents-end 3584 :post-blank 1 :post-affiliated 3563 :mode nil :granularity nil :parent #187) #("You also need to set\n" 0 21 (:parent #196))) (fixed-width (:begin 3585 :end 3608 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3585 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3608 :end 3688 :contents-begin 3608 :contents-end 3687 :post-blank 1 :post-affiliated 3608 :mode nil :granularity nil :parent #187) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #198))) (paragraph (:begin 3688 :end 3757 :contents-begin 3688 :contents-end 3756 :post-blank 1 :post-affiliated 3688 :mode nil :granularity nil :parent #187) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #199))) (fixed-width (:begin 3757 :end 3872 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3757 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3872 :end 3950 :contents-begin 3872 :contents-end 3949 :post-blank 1 :post-affiliated 3872 :mode nil :granularity nil :parent #187) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #201))) (fixed-width (:begin 3950 :end 4060 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3950 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4060 :end 4087 :contents-begin 4060 :contents-end 4086 :post-blank 1 :post-affiliated 4060 :mode nil :granularity nil :parent #187) #("When you get errors like:\n" 0 26 (:parent #203))) (fixed-width (:begin 4087 :end 4201 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4087 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4201 :end 4222 :contents-begin 4201 :contents-end 4221 :post-blank 1 :post-affiliated 4201 :mode nil :granularity nil :parent #187) #("you may need to set\n" 0 20 (:parent #205))) (fixed-width (:begin 4222 :end 4249 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4222 :mode nil :granularity nil :parent #187)))) (headline (:raw-value "Load the small database in MySQL" :begin 4250 :end 5782 :pre-blank 1 :contents-begin 4287 :contents-end 5781 :robust-begin 4289 :robust-end 5779 :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 4250 :title (#("Load the small database in MySQL" 0 32 (:parent #185))) :mode nil :granularity nil :parent #181) (section (:begin 4287 :end 5782 :contents-begin 4287 :contents-end 5781 :robust-begin 4287 :robust-end 5779 :post-blank 1 :post-affiliated 4287 :mode section :granularity nil :parent #185) (paragraph (:begin 4287 :end 4594 :contents-begin 4287 :contents-end 4593 :post-blank 1 :post-affiliated 4287 :mode planning :granularity nil :parent #188) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #191)) (subscript (:begin 4450 :end 4457 :use-brackets-p nil :contents-begin 4451 :contents-end 4457 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #195))) (subscript (:begin 4457 :end 4459 :use-brackets-p nil :contents-begin 4458 :contents-end 4459 :post-blank 0 :parent #191) #("s" 0 1 (:parent #196))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #191)) (subscript (:begin 4535 :end 4542 :use-brackets-p nil :contents-begin 4536 :contents-end 4542 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 4542 :end 4548 :use-brackets-p nil :contents-begin 4543 :contents-end 4548 :post-blank 0 :parent #191) #("plant" 0 5 (:parent #199))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #191))) (paragraph (:begin 4594 :end 4622 :contents-begin 4594 :contents-end 4621 :post-blank 1 :post-affiliated 4594 :mode nil :granularity nil :parent #188) #("Download one database from\n" 0 27 (:parent #192))) (paragraph (:begin 4622 :end 4670 :contents-begin 4622 :contents-end 4669 :post-blank 1 :post-affiliated 4622 :mode nil :granularity nil :parent #188) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4622 :end 4668 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4670 :end 4729 :contents-begin 4670 :contents-end 4728 :post-blank 1 :post-affiliated 4670 :mode nil :granularity nil :parent #188) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4670 :end 4727 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 4729 :end 4748 :contents-begin 4729 :contents-end 4747 :post-blank 1 :post-affiliated 4729 :mode nil :granularity nil :parent #188) #("Check the md5sum.\n" 0 18 (:parent #195))) (paragraph (:begin 4748 :end 4819 :contents-begin 4748 :contents-end 4818 :post-blank 1 :post-affiliated 4748 :mode nil :granularity nil :parent #188) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #196))) (fixed-width (:begin 4819 :end 4920 :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 4819 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4920 :end 4967 :contents-begin 4920 :contents-end 4966 :post-blank 1 :post-affiliated 4920 :mode nil :granularity nil :parent #188) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #198))) (fixed-width (:begin 4967 :end 4984 :value "myslq -u root" :post-blank 2 :post-affiliated 4967 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4984 :end 4989 :contents-begin 4984 :contents-end 4988 :post-blank 1 :post-affiliated 4984 :mode nil :granularity nil :parent #188) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 4989 :end 5215 :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 4989 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5215 :end 5280 :contents-begin 5215 :contents-end 5279 :post-blank 1 :post-affiliated 5215 :mode nil :granularity nil :parent #188) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 5280 :end 5379 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5280 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5379 :end 5486 :contents-begin 5379 :contents-end 5485 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #188) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 5486 :end 5649 :contents-begin 5486 :contents-end 5648 :post-blank 1 :post-affiliated 5486 :mode nil :granularity nil :parent #188) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 5649 :end 5781 :contents-begin 5649 :contents-end 5781 :post-blank 0 :post-affiliated 5649 :mode nil :granularity nil :parent #188) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript 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:end 5946 :contents-begin 5806 :contents-end 5945 :robust-begin 5806 :robust-end 5943 :post-blank 1 :post-affiliated 5806 :mode section :granularity nil :parent #182) (paragraph (:begin 5806 :end 5867 :contents-begin 5806 :contents-end 5866 :post-blank 1 :post-affiliated 5806 :mode planning :granularity nil :parent #185) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #188))) (paragraph (:begin 5867 :end 5945 :contents-begin 5897 :contents-end 5945 :post-blank 0 :post-affiliated 5897 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #185) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5897 :end 5944 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))))) (headline (:raw-value "Working with the GN2 source code" :begin 5946 :end 6008 :pre-blank 1 :contents-begin 5982 :contents-end 6007 :robust-begin 5984 :robust-end 6005 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5946 :title (#("Working with the GN2 source code" 0 32 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 5982 :end 6008 :contents-begin 5982 :contents-end 6007 :robust-begin 5982 :robust-end 6005 :post-blank 1 :post-affiliated 5982 :mode section :granularity nil :parent #183) (paragraph (:begin 5982 :end 6007 :contents-begin 5982 :contents-end 6007 :post-blank 0 :post-affiliated 5982 :mode planning :granularity nil :parent #186) #("See " 0 4 (:parent #189)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5986 :end 6005 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "Read more" :begin 6008 :end 6158 :pre-blank 1 :contents-begin 6021 :contents-end 6157 :robust-begin 6023 :robust-end 6155 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6008 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 6021 :end 6158 :contents-begin 6021 :contents-end 6157 :robust-begin 6021 :robust-end 6155 :post-blank 1 :post-affiliated 6021 :mode section :granularity nil :parent #184) (paragraph (:begin 6021 :end 6157 :contents-begin 6021 :contents-end 6157 :post-blank 0 :post-affiliated 6021 :mode planning :granularity nil :parent #187) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #190)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6076 :end 6096 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #190))))) (headline (:raw-value "Trouble shooting" :begin 6158 :end 8609 :pre-blank 1 :contents-begin 6178 :contents-end 8607 :robust-begin 6180 :robust-end 8605 :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 6158 :title (#("Trouble shooting" 0 16 (:parent #185))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6178 :end 6712 :pre-blank 1 :contents-begin 6218 :contents-end 6712 :robust-begin 6220 :robust-end 6710 :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 6178 :title (#("ImportError: No module named jinja2" 0 35 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 6218 :end 6712 :contents-begin 6218 :contents-end 6712 :robust-begin 6218 :robust-end 6710 :post-blank 0 :post-affiliated 6218 :mode section :granularity nil :parent #188) (paragraph (:begin 6218 :end 6453 :contents-begin 6218 :contents-end 6452 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #191) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #194)) (subscript (:begin 6385 :end 6391 :use-brackets-p nil :contents-begin 6386 :contents-end 6390 :post-blank 1 :parent #194) #("PATH" 0 4 (:parent #198))) #("and R" 0 5 (:parent #194)) (subscript (:begin 6396 :end 6401 :use-brackets-p nil :contents-begin 6397 :contents-end 6401 :post-blank 0 :parent #194) #("LIBS" 0 4 (:parent #200))) (subscript (:begin 6401 :end 6407 :use-brackets-p nil :contents-begin 6402 :contents-end 6406 :post-blank 1 :parent #194) #("SITE" 0 4 (:parent #201))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #194))) (fixed-width (:begin 6453 :end 6484 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6453 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6484 :end 6500 :contents-begin 6484 :contents-end 6499 :post-blank 1 :post-affiliated 6484 :mode nil :granularity nil :parent #191) #("On one system:\n" 0 15 (:parent #196))) (fixed-width (:begin 6500 :end 6688 :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 6500 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6688 :end 6712 :contents-begin 6688 :contents-end 6712 :post-blank 0 :post-affiliated 6688 :mode nil :granularity nil :parent #191) #("and perhaps a few more.\n" 0 24 (:parent #198))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6712 :end 7208 :pre-blank 1 :contents-begin 6821 :contents-end 7207 :robust-begin 6823 :robust-end 7205 :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 6712 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #189)) (subscript (:begin 6755 :end 6760 :use-brackets-p nil :contents-begin 6756 :contents-end 6760 :post-blank 0 :parent #189) #("data" 0 4 (:parent #231))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #189)) (subscript (:begin 6803 :end 6809 :use-brackets-p nil :contents-begin 6804 :contents-end 6809 :post-blank 0 :parent #189) #("files" 0 5 (:parent #233))) #("/genotype'" 0 10 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 6821 :end 7208 :contents-begin 6821 :contents-end 7207 :robust-begin 6821 :robust-end 7205 :post-blank 1 :post-affiliated 6821 :mode section :granularity nil :parent #189) (paragraph (:begin 6821 :end 7043 :contents-begin 6821 :contents-end 7042 :post-blank 1 :post-affiliated 6821 :mode planning :granularity nil :parent #192) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #195)) (subscript (:begin 6870 :end 6875 :use-brackets-p nil :contents-begin 6871 :contents-end 6875 :post-blank 0 :parent #195) #("data" 0 4 (:parent #199))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #195)) (subscript (:begin 6999 :end 7012 :use-brackets-p nil :contents-begin 7000 :contents-end 7011 :post-blank 1 :parent #195) #("settings.py" 0 11 (:parent #201))) #("(see above in\nthis document).\n" 0 30 (:parent #195))) (paragraph (:begin 7043 :end 7117 :contents-begin 7043 :contents-end 7116 :post-blank 1 :post-affiliated 7043 :mode nil :granularity nil :parent #192) #("You can use the GENENETWORK" 0 27 (:parent #196)) (subscript (:begin 7070 :end 7077 :use-brackets-p nil :contents-begin 7071 :contents-end 7076 :post-blank 1 :parent #196) #("FILES" 0 5 (:parent #200))) #("switch to set the datadir, for example\n" 0 39 (:parent #196))) (fixed-width (:begin 7117 :end 7207 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7117 :mode nil :granularity nil :parent #192)))) (headline (:raw-value "Can't run a module" :begin 7208 :end 7442 :pre-blank 1 :contents-begin 7231 :contents-end 7442 :robust-begin 7233 :robust-end 7440 :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 7208 :title (#("Can't run a module" 0 18 (:parent #190))) :mode nil :granularity nil :parent #185) (section (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :robust-begin 7231 :robust-end 7440 :post-blank 0 :post-affiliated 7231 :mode section :granularity nil :parent #190) (paragraph (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :post-blank 0 :post-affiliated 7231 :mode planning :granularity nil :parent #193) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #196))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7442 :end 7943 :pre-blank 1 :contents-begin 7474 :contents-end 7942 :robust-begin 7476 :robust-end 7940 :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 7442 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #191))) :mode nil :granularity nil :parent #185) (section (:begin 7474 :end 7943 :contents-begin 7474 :contents-end 7942 :robust-begin 7474 :robust-end 7940 :post-blank 1 :post-affiliated 7474 :mode section :granularity nil :parent #191) (paragraph (:begin 7474 :end 7486 :contents-begin 7474 :contents-end 7485 :post-blank 1 :post-affiliated 7474 :mode planning :granularity nil :parent #194) #("This error\n" 0 11 (:parent #197))) (fixed-width (:begin 7486 :end 7566 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7486 :mode nil :granularity nil :parent #194)) (paragraph (:begin 7566 :end 7697 :contents-begin 7566 :contents-end 7696 :post-blank 1 :post-affiliated 7566 :mode nil :granularity nil :parent #194) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #199))) (paragraph (:begin 7697 :end 7942 :contents-begin 7697 :contents-end 7942 :post-blank 0 :post-affiliated 7697 :mode nil :granularity nil :parent #194) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #200)) (subscript (:begin 7760 :end 7765 :use-brackets-p nil :contents-begin 7761 :contents-end 7765 :post-blank 0 :parent #200) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 7765 :end 7770 :use-brackets-p nil :contents-begin 7766 :contents-end 7770 :post-blank 0 :parent #200) #("SITE" 0 4 (:parent #205))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #200))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7943 :end 8609 :pre-blank 1 :contents-begin 7995 :contents-end 8607 :robust-begin 7997 :robust-end 8605 :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 7943 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #192))) :mode nil :granularity nil :parent #185) (section (:begin 7995 :end 8609 :contents-begin 7995 :contents-end 8607 :robust-begin 7995 :robust-end 8605 :post-blank 2 :post-affiliated 7995 :mode section :granularity nil :parent #192) (paragraph (:begin 7995 :end 8016 :contents-begin 7995 :contents-end 8015 :post-blank 1 :post-affiliated 7995 :mode planning :granularity nil :parent #195) #("The following error\n" 0 20 (:parent #198))) (fixed-width (:begin 8016 :end 8211 :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 8016 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8211 :end 8369 :contents-begin 8211 :contents-end 8368 :post-blank 1 :post-affiliated 8211 :mode nil :granularity nil :parent #195) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #200))) (fixed-width (:begin 8369 :end 8391 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8369 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8391 :end 8448 :contents-begin 8391 :contents-end 8447 :post-blank 1 :post-affiliated 8391 :mode nil :granularity nil :parent #195) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #202))) (fixed-width (:begin 8448 :end 8470 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8448 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8470 :end 8541 :contents-begin 8470 :contents-end 8540 :post-blank 1 :post-affiliated 8470 :mode nil :granularity nil :parent #195) #("if that works run genenetwork after setting SQL" 0 47 (:parent #204)) (subscript (:begin 8517 :end 8522 :use-brackets-p nil :contents-begin 8518 :contents-end 8521 :post-blank 1 :parent #204) #("URI" 0 3 (:parent #208))) #("to something like\n" 0 18 (:parent #204))) (fixed-width (:begin 8541 :end 8607 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8541 :mode nil :granularity nil :parent #195))))) (headline (:raw-value "IRC session" :begin 8609 :end 15256 :pre-blank 1 :contents-begin 8624 :contents-end 15256 :robust-begin 8626 :robust-end 15254 :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 8609 :title (#("IRC session" 0 11 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 8624 :end 15256 :contents-begin 8624 :contents-end 15256 :robust-begin 8624 :robust-end 15254 :post-blank 0 :post-affiliated 8624 :mode section :granularity nil :parent #186) (paragraph (:begin 8624 :end 8733 :contents-begin 8624 :contents-end 8732 :post-blank 1 :post-affiliated 8624 :mode planning :granularity nil :parent #189) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #192))) (paragraph (:begin 8733 :end 9294 :contents-begin 8733 :contents-end 9293 :post-blank 1 :post-affiliated 8733 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 8740 :end 8744 :use-brackets-p nil :contents-begin 8741 :contents-end 8744 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #193))) (paragraph (:begin 9294 :end 9384 :contents-begin 9294 :contents-end 9383 :post-blank 1 :post-affiliated 9294 :mode nil :granularity nil :parent #189) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 9384 :end 9529 :contents-begin 9384 :contents-end 9528 :post-blank 1 :post-affiliated 9384 :mode nil :granularity nil :parent #189) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 9414 :end 9422 :use-brackets-p nil :contents-begin 9415 :contents-end 9422 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 9422 :end 9427 :use-brackets-p nil :contents-begin 9423 :contents-end 9427 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 9529 :end 9825 :contents-begin 9529 :contents-end 9824 :post-blank 1 :post-affiliated 9529 :mode nil :granularity nil :parent #189) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #196))) (paragraph (:begin 9825 :end 11018 :contents-begin 9825 :contents-end 11017 :post-blank 1 :post-affiliated 9825 :mode nil :granularity nil :parent #189) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #197)) (subscript (:begin 10578 :end 10586 :use-brackets-p nil :contents-begin 10579 :contents-end 10586 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 10586 :end 10591 :use-brackets-p nil :contents-begin 10587 :contents-end 10591 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #197))) (paragraph (:begin 11018 :end 11222 :contents-begin 11018 :contents-end 11221 :post-blank 1 :post-affiliated 11018 :mode nil :granularity nil :parent #189) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #198))) (paragraph (:begin 11222 :end 15256 :contents-begin 11222 :contents-end 15256 :post-blank 0 :post-affiliated 11222 :mode nil :granularity nil :parent #189) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 11270 :end 12179 :post-blank 0 :contents-begin 11271 :contents-end 12178 :parent #199) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #203))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #199)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12979 :end 13044 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13292 :end 13325 :contents-begin nil :contents-end nil :post-blank 1 :parent #199)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #199)) (subscript (:begin 13549 :end 13557 :use-brackets-p nil :contents-begin 13550 :contents-end 13557 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #209))) (subscript (:begin 13557 :end 13562 :use-brackets-p nil :contents-begin 13558 :contents-end 13562 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #210))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #199)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13678 :end 13705 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #199)) (subscript (:begin 14275 :end 14283 :use-brackets-p nil :contents-begin 14276 :contents-end 14283 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #214))) (subscript (:begin 14283 :end 14288 :use-brackets-p nil :contents-begin 14284 :contents-end 14288 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #215))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #199)) (subscript (:begin 14947 :end 14955 :use-brackets-p nil :contents-begin 14948 :contents-end 14955 :post-blank 0 :parent #199) #("PACKAGE" 0 7 (:parent #217))) (subscript (:begin 14955 :end 14960 :use-brackets-p nil :contents-begin 14956 :contents-end 14960 :post-blank 0 :parent #199) #("PATH" 0 4 (:parent #218))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #199)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 15074 :end 15106 :contents-begin nil :contents-end nil :post-blank 0 :parent #199)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n" 0 150 (:parent #199))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 181 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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 "Running Redis" :begin 2849 :end 2931 :pre-blank 1 :contents-begin 2866 :contents-end 2930 :robust-begin 2868 :robust-end 2928 :level 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 (#("Running Redis" 0 13 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2866 :end 2931 :contents-begin 2866 :contents-end 2930 :robust-begin 2866 :robust-end 2928 :post-blank 1 :post-affiliated 2866 :mode section :granularity nil :parent #346) (paragraph (:begin 2866 :end 2913 :contents-begin 2866 :contents-end 2912 :post-blank 1 :post-affiliated 2866 :mode planning :granularity nil :parent #349) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #352))) (fixed-width (:begin 2913 :end 2930 :value "appendonly yes" :post-blank 1 :post-affiliated 2913 :mode nil :granularity nil :parent #349)))) (headline (:raw-value "Run MariaDB server" :begin 2931 :end 5782 :pre-blank 0 :contents-begin 2952 :contents-end 5781 :robust-begin 2954 :robust-end 5779 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2931 :title (#("Run MariaDB server" 0 18 (:parent #347))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2952 :end 4250 :pre-blank 1 :contents-begin 2986 :contents-end 4249 :robust-begin 2988 :robust-end 4247 :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 2952 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #350))) :mode section :granularity nil :parent #347) (section (:begin 2986 :end 4250 :contents-begin 2986 :contents-end 4249 :robust-begin 2986 :robust-end 4247 :post-blank 1 :post-affiliated 2986 :mode section :granularity nil :parent #350) (paragraph (:begin 2986 :end 3015 :contents-begin 2986 :contents-end 3014 :post-blank 1 :post-affiliated 2986 :mode planning :granularity nil :parent #353) (italic (:begin 2986 :end 3013 :post-blank 0 :contents-begin 2987 :contents-end 3012 :parent #356) #("Note: we moved to MariaDB" 0 25 (:parent #359))) #("\n" 0 1 (:parent #356))) (paragraph (:begin 3015 :end 3152 :contents-begin 3015 :contents-end 3151 :post-blank 1 :post-affiliated 3015 :mode nil :granularity nil :parent #353) #("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 #357))) (paragraph (:begin 3152 :end 3179 :contents-begin 3152 :contents-end 3178 :post-blank 1 :post-affiliated 3152 :mode nil :granularity nil :parent #353) #("As root configure and run\n" 0 26 (:parent #358))) (src-block (:language "bash" :switches nil :parameters nil :begin 3179 :end 3475 :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 3179 :mode nil :granularity nil :parent #353)) (paragraph (:begin 3475 :end 3523 :contents-begin 3475 :contents-end 3522 :post-blank 1 :post-affiliated 3475 :mode nil :granularity nil :parent #353) #("If you want to run as root you may have to set\n" 0 47 (:parent #360))) (fixed-width (:begin 3523 :end 3563 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3523 :mode nil :granularity nil :parent #353)) (paragraph (:begin 3563 :end 3585 :contents-begin 3563 :contents-end 3584 :post-blank 1 :post-affiliated 3563 :mode nil :granularity nil :parent #353) #("You also need to set\n" 0 21 (:parent #362))) (fixed-width (:begin 3585 :end 3608 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3585 :mode nil :granularity nil :parent #353)) (paragraph (:begin 3608 :end 3688 :contents-begin 3608 :contents-end 3687 :post-blank 1 :post-affiliated 3608 :mode nil :granularity nil :parent #353) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #364))) (paragraph (:begin 3688 :end 3757 :contents-begin 3688 :contents-end 3756 :post-blank 1 :post-affiliated 3688 :mode nil :granularity nil :parent #353) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #365))) (fixed-width (:begin 3757 :end 3872 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3757 :mode nil :granularity nil :parent #353)) (paragraph (:begin 3872 :end 3950 :contents-begin 3872 :contents-end 3949 :post-blank 1 :post-affiliated 3872 :mode nil :granularity nil :parent #353) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #367))) (fixed-width (:begin 3950 :end 4060 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3950 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4060 :end 4087 :contents-begin 4060 :contents-end 4086 :post-blank 1 :post-affiliated 4060 :mode nil :granularity nil :parent #353) #("When you get errors like:\n" 0 26 (:parent #369))) (fixed-width (:begin 4087 :end 4201 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4087 :mode nil :granularity nil :parent #353)) (paragraph (:begin 4201 :end 4222 :contents-begin 4201 :contents-end 4221 :post-blank 1 :post-affiliated 4201 :mode nil :granularity nil :parent #353) #("you may need to set\n" 0 20 (:parent #371))) (fixed-width (:begin 4222 :end 4249 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4222 :mode nil :granularity nil :parent #353)))) (headline (:raw-value "Load the small database in MySQL" :begin 4250 :end 5782 :pre-blank 1 :contents-begin 4287 :contents-end 5781 :robust-begin 4289 :robust-end 5779 :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 4250 :title (#("Load the small database in MySQL" 0 32 (:parent #351))) :mode nil :granularity nil :parent #347) (section (:begin 4287 :end 5782 :contents-begin 4287 :contents-end 5781 :robust-begin 4287 :robust-end 5779 :post-blank 1 :post-affiliated 4287 :mode section :granularity nil :parent #351) (paragraph (:begin 4287 :end 4594 :contents-begin 4287 :contents-end 4593 :post-blank 1 :post-affiliated 4287 :mode planning :granularity nil :parent #354) #("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 #357)) (subscript (:begin 4450 :end 4457 :use-brackets-p nil :contents-begin 4451 :contents-end 4457 :post-blank 0 :parent #357) #("webqtl" 0 6 (:parent #361))) (subscript (:begin 4457 :end 4459 :use-brackets-p nil :contents-begin 4458 :contents-end 4459 :post-blank 0 :parent #357) #("s" 0 1 (:parent #362))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #357)) (subscript (:begin 4535 :end 4542 :use-brackets-p nil :contents-begin 4536 :contents-end 4542 :post-blank 0 :parent #357) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 4542 :end 4548 :use-brackets-p nil :contents-begin 4543 :contents-end 4548 :post-blank 0 :parent #357) #("plant" 0 5 (:parent #365))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #357))) (paragraph (:begin 4594 :end 4622 :contents-begin 4594 :contents-end 4621 :post-blank 1 :post-affiliated 4594 :mode nil :granularity nil :parent #354) #("Download one database from\n" 0 27 (:parent #358))) (paragraph (:begin 4622 :end 4670 :contents-begin 4622 :contents-end 4669 :post-blank 1 :post-affiliated 4622 :mode nil :granularity nil :parent #354) (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 4622 :end 4668 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4670 :end 4729 :contents-begin 4670 :contents-end 4728 :post-blank 1 :post-affiliated 4670 :mode nil :granularity nil :parent #354) (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 4670 :end 4727 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 4729 :end 4748 :contents-begin 4729 :contents-end 4747 :post-blank 1 :post-affiliated 4729 :mode nil :granularity nil :parent #354) #("Check the md5sum.\n" 0 18 (:parent #361))) (paragraph (:begin 4748 :end 4819 :contents-begin 4748 :contents-end 4818 :post-blank 1 :post-affiliated 4748 :mode nil :granularity nil :parent #354) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #362))) (fixed-width (:begin 4819 :end 4920 :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 4819 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4920 :end 4967 :contents-begin 4920 :contents-end 4966 :post-blank 1 :post-affiliated 4920 :mode nil :granularity nil :parent #354) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #364))) (fixed-width (:begin 4967 :end 4984 :value "myslq -u root" :post-blank 2 :post-affiliated 4967 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4984 :end 4989 :contents-begin 4984 :contents-end 4988 :post-blank 1 :post-affiliated 4984 :mode nil :granularity nil :parent #354) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 4989 :end 5215 :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 4989 :mode nil :granularity nil :parent #354)) (paragraph (:begin 5215 :end 5280 :contents-begin 5215 :contents-end 5279 :post-blank 1 :post-affiliated 5215 :mode nil :granularity nil :parent #354) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5280 :end 5379 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5280 :mode nil :granularity nil :parent #354)) (paragraph (:begin 5379 :end 5486 :contents-begin 5379 :contents-end 5485 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #354) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 5486 :end 5649 :contents-begin 5486 :contents-end 5648 :post-blank 1 :post-affiliated 5486 :mode nil :granularity nil :parent #354) #("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 #371))) (paragraph (:begin 5649 :end 5781 :contents-begin 5649 :contents-end 5781 :post-blank 0 :post-affiliated 5649 :mode nil :granularity nil :parent #354) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 5700 :end 5707 :use-brackets-p nil :contents-begin 5701 :contents-end 5707 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 5707 :end 5709 :use-brackets-p nil :contents-begin 5708 :contents-end 5709 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 5748 :end 5761 :use-brackets-p nil :contents-begin 5749 :contents-end 5760 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5782 :end 5946 :pre-blank 1 :contents-begin 5806 :contents-end 5945 :robust-begin 5808 :robust-end 5943 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5782 :title (#("GN2 Dependency Graph" 0 20 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5806 :end 5946 :contents-begin 5806 :contents-end 5945 :robust-begin 5806 :robust-end 5943 :post-blank 1 :post-affiliated 5806 :mode section :granularity nil :parent #348) (paragraph (:begin 5806 :end 5867 :contents-begin 5806 :contents-end 5866 :post-blank 1 :post-affiliated 5806 :mode planning :granularity nil :parent #351) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #354))) (paragraph (:begin 5867 :end 5945 :contents-begin 5897 :contents-end 5945 :post-blank 0 :post-affiliated 5897 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #351) (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 5897 :end 5944 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))))) (headline (:raw-value "Working with the GN2 source code" :begin 5946 :end 6008 :pre-blank 1 :contents-begin 5982 :contents-end 6007 :robust-begin 5984 :robust-end 6005 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5946 :title (#("Working with the GN2 source code" 0 32 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 5982 :end 6008 :contents-begin 5982 :contents-end 6007 :robust-begin 5982 :robust-end 6005 :post-blank 1 :post-affiliated 5982 :mode section :granularity nil :parent #349) (paragraph (:begin 5982 :end 6007 :contents-begin 5982 :contents-end 6007 :post-blank 0 :post-affiliated 5982 :mode planning :granularity nil :parent #352) #("See " 0 4 (:parent #355)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5986 :end 6005 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(".\n" 0 2 (:parent #355))))) (headline (:raw-value "Read more" :begin 6008 :end 6158 :pre-blank 1 :contents-begin 6021 :contents-end 6157 :robust-begin 6023 :robust-end 6155 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6008 :title (#("Read more" 0 9 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6021 :end 6158 :contents-begin 6021 :contents-end 6157 :robust-begin 6021 :robust-end 6155 :post-blank 1 :post-affiliated 6021 :mode section :granularity nil :parent #350) (paragraph (:begin 6021 :end 6157 :contents-begin 6021 :contents-end 6157 :post-blank 0 :post-affiliated 6021 :mode planning :granularity nil :parent #353) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #356)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6076 :end 6096 :contents-begin nil :contents-end nil :post-blank 0 :parent #356)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #356))))) (headline (:raw-value "Trouble shooting" :begin 6158 :end 8609 :pre-blank 1 :contents-begin 6178 :contents-end 8607 :robust-begin 6180 :robust-end 8605 :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 6158 :title (#("Trouble shooting" 0 16 (:parent #351))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6178 :end 6712 :pre-blank 1 :contents-begin 6218 :contents-end 6712 :robust-begin 6220 :robust-end 6710 :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 6178 :title (#("ImportError: No module named jinja2" 0 35 (:parent #354))) :mode section :granularity nil :parent #351) (section (:begin 6218 :end 6712 :contents-begin 6218 :contents-end 6712 :robust-begin 6218 :robust-end 6710 :post-blank 0 :post-affiliated 6218 :mode section :granularity nil :parent #354) (paragraph (:begin 6218 :end 6453 :contents-begin 6218 :contents-end 6452 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 6385 :end 6391 :use-brackets-p nil :contents-begin 6386 :contents-end 6390 :post-blank 1 :parent #360) #("PATH" 0 4 (:parent #364))) #("and R" 0 5 (:parent #360)) (subscript (:begin 6396 :end 6401 :use-brackets-p nil :contents-begin 6397 :contents-end 6401 :post-blank 0 :parent #360) #("LIBS" 0 4 (:parent #366))) (subscript (:begin 6401 :end 6407 :use-brackets-p nil :contents-begin 6402 :contents-end 6406 :post-blank 1 :parent #360) #("SITE" 0 4 (:parent #367))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #360))) (fixed-width (:begin 6453 :end 6484 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6453 :mode nil :granularity nil :parent #357)) (paragraph (:begin 6484 :end 6500 :contents-begin 6484 :contents-end 6499 :post-blank 1 :post-affiliated 6484 :mode nil :granularity nil :parent #357) #("On one system:\n" 0 15 (:parent #362))) (fixed-width (:begin 6500 :end 6688 :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 6500 :mode nil :granularity nil :parent #357)) (paragraph (:begin 6688 :end 6712 :contents-begin 6688 :contents-end 6712 :post-blank 0 :post-affiliated 6688 :mode nil :granularity nil :parent #357) #("and perhaps a few more.\n" 0 24 (:parent #364))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6712 :end 7208 :pre-blank 1 :contents-begin 6821 :contents-end 7207 :robust-begin 6823 :robust-end 7205 :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 6712 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #355)) (subscript (:begin 6755 :end 6760 :use-brackets-p nil :contents-begin 6756 :contents-end 6760 :post-blank 0 :parent #355) #("data" 0 4 (:parent #397))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #355)) (subscript (:begin 6803 :end 6809 :use-brackets-p nil :contents-begin 6804 :contents-end 6809 :post-blank 0 :parent #355) #("files" 0 5 (:parent #399))) #("/genotype'" 0 10 (:parent #355))) :mode nil :granularity nil :parent #351) (section (:begin 6821 :end 7208 :contents-begin 6821 :contents-end 7207 :robust-begin 6821 :robust-end 7205 :post-blank 1 :post-affiliated 6821 :mode section :granularity nil :parent #355) (paragraph (:begin 6821 :end 7043 :contents-begin 6821 :contents-end 7042 :post-blank 1 :post-affiliated 6821 :mode planning :granularity nil :parent #358) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #361)) (subscript (:begin 6870 :end 6875 :use-brackets-p nil :contents-begin 6871 :contents-end 6875 :post-blank 0 :parent #361) #("data" 0 4 (:parent #365))) #(". 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 #361)) (subscript (:begin 6999 :end 7012 :use-brackets-p nil :contents-begin 7000 :contents-end 7011 :post-blank 1 :parent #361) #("settings.py" 0 11 (:parent #367))) #("(see above in\nthis document).\n" 0 30 (:parent #361))) (paragraph (:begin 7043 :end 7117 :contents-begin 7043 :contents-end 7116 :post-blank 1 :post-affiliated 7043 :mode nil :granularity nil :parent #358) #("You can use the GENENETWORK" 0 27 (:parent #362)) (subscript (:begin 7070 :end 7077 :use-brackets-p nil :contents-begin 7071 :contents-end 7076 :post-blank 1 :parent #362) #("FILES" 0 5 (:parent #366))) #("switch to set the datadir, for example\n" 0 39 (:parent #362))) (fixed-width (:begin 7117 :end 7207 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7117 :mode nil :granularity nil :parent #358)))) (headline (:raw-value "Can't run a module" :begin 7208 :end 7442 :pre-blank 1 :contents-begin 7231 :contents-end 7442 :robust-begin 7233 :robust-end 7440 :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 7208 :title (#("Can't run a module" 0 18 (:parent #356))) :mode nil :granularity nil :parent #351) (section (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :robust-begin 7231 :robust-end 7440 :post-blank 0 :post-affiliated 7231 :mode section :granularity nil :parent #356) (paragraph (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :post-blank 0 :post-affiliated 7231 :mode planning :granularity nil :parent #359) #("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 #362))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7442 :end 7943 :pre-blank 1 :contents-begin 7474 :contents-end 7942 :robust-begin 7476 :robust-end 7940 :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 7442 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #357))) :mode nil :granularity nil :parent #351) (section (:begin 7474 :end 7943 :contents-begin 7474 :contents-end 7942 :robust-begin 7474 :robust-end 7940 :post-blank 1 :post-affiliated 7474 :mode section :granularity nil :parent #357) (paragraph (:begin 7474 :end 7486 :contents-begin 7474 :contents-end 7485 :post-blank 1 :post-affiliated 7474 :mode planning :granularity nil :parent #360) #("This error\n" 0 11 (:parent #363))) (fixed-width (:begin 7486 :end 7566 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7486 :mode nil :granularity nil :parent #360)) (paragraph (:begin 7566 :end 7697 :contents-begin 7566 :contents-end 7696 :post-blank 1 :post-affiliated 7566 :mode nil :granularity nil :parent #360) #("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 #365))) (paragraph (:begin 7697 :end 7942 :contents-begin 7697 :contents-end 7942 :post-blank 0 :post-affiliated 7697 :mode nil :granularity nil :parent #360) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #366)) (subscript (:begin 7760 :end 7765 :use-brackets-p nil :contents-begin 7761 :contents-end 7765 :post-blank 0 :parent #366) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 7765 :end 7770 :use-brackets-p nil :contents-begin 7766 :contents-end 7770 :post-blank 0 :parent #366) #("SITE" 0 4 (:parent #371))) #(". 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 #366))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7943 :end 8609 :pre-blank 1 :contents-begin 7995 :contents-end 8607 :robust-begin 7997 :robust-end 8605 :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 7943 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #358))) :mode nil :granularity nil :parent #351) (section (:begin 7995 :end 8609 :contents-begin 7995 :contents-end 8607 :robust-begin 7995 :robust-end 8605 :post-blank 2 :post-affiliated 7995 :mode section :granularity nil :parent #358) (paragraph (:begin 7995 :end 8016 :contents-begin 7995 :contents-end 8015 :post-blank 1 :post-affiliated 7995 :mode planning :granularity nil :parent #361) #("The following error\n" 0 20 (:parent #364))) (fixed-width (:begin 8016 :end 8211 :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 8016 :mode nil :granularity nil :parent #361)) (paragraph (:begin 8211 :end 8369 :contents-begin 8211 :contents-end 8368 :post-blank 1 :post-affiliated 8211 :mode nil :granularity nil :parent #361) #("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 #366))) (fixed-width (:begin 8369 :end 8391 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8369 :mode nil :granularity nil :parent #361)) (paragraph (:begin 8391 :end 8448 :contents-begin 8391 :contents-end 8447 :post-blank 1 :post-affiliated 8391 :mode nil :granularity nil :parent #361) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #368))) (fixed-width (:begin 8448 :end 8470 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8448 :mode nil :granularity nil :parent #361)) (paragraph (:begin 8470 :end 8541 :contents-begin 8470 :contents-end 8540 :post-blank 1 :post-affiliated 8470 :mode nil :granularity nil :parent #361) #("if that works run genenetwork after setting SQL" 0 47 (:parent #370)) (subscript (:begin 8517 :end 8522 :use-brackets-p nil :contents-begin 8518 :contents-end 8521 :post-blank 1 :parent #370) #("URI" 0 3 (:parent #374))) #("to something like\n" 0 18 (:parent #370))) (fixed-width (:begin 8541 :end 8607 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8541 :mode nil :granularity nil :parent #361))))) (headline (:raw-value "IRC session" :begin 8609 :end 15256 :pre-blank 1 :contents-begin 8624 :contents-end 15256 :robust-begin 8626 :robust-end 15254 :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 8609 :title (#("IRC session" 0 11 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 8624 :end 15256 :contents-begin 8624 :contents-end 15256 :robust-begin 8624 :robust-end 15254 :post-blank 0 :post-affiliated 8624 :mode section :granularity nil :parent #352) (paragraph (:begin 8624 :end 8733 :contents-begin 8624 :contents-end 8732 :post-blank 1 :post-affiliated 8624 :mode planning :granularity nil :parent #355) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #358))) (paragraph (:begin 8733 :end 9294 :contents-begin 8733 :contents-end 9293 :post-blank 1 :post-affiliated 8733 :mode nil :granularity nil :parent #355) #("#+begin" 0 7 (:parent #359)) (subscript (:begin 8740 :end 8744 :use-brackets-p nil :contents-begin 8741 :contents-end 8744 :post-blank 0 :parent #359) #("src" 0 3 (:parent #363))) #("\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 #359))) (paragraph (:begin 9294 :end 9384 :contents-begin 9294 :contents-end 9383 :post-blank 1 :post-affiliated 9294 :mode nil :granularity nil :parent #355) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #360))) (paragraph (:begin 9384 :end 9529 :contents-begin 9384 :contents-end 9528 :post-blank 1 :post-affiliated 9384 :mode nil :granularity nil :parent #355) #(" yes\n env GUIX" 0 30 (:parent #361)) (subscript (:begin 9414 :end 9422 :use-brackets-p nil :contents-begin 9415 :contents-end 9422 :post-blank 0 :parent #361) #("PACKAGE" 0 7 (:parent #365))) (subscript (:begin 9422 :end 9427 :use-brackets-p nil :contents-begin 9423 :contents-end 9427 :post-blank 0 :parent #361) #("PATH" 0 4 (:parent #366))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #361))) (paragraph (:begin 9529 :end 9825 :contents-begin 9529 :contents-end 9824 :post-blank 1 :post-affiliated 9529 :mode nil :granularity nil :parent #355) #("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 #362))) (paragraph (:begin 9825 :end 11018 :contents-begin 9825 :contents-end 11017 :post-blank 1 :post-affiliated 9825 :mode nil :granularity nil :parent #355) #(" 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 #363)) (subscript (:begin 10578 :end 10586 :use-brackets-p nil :contents-begin 10579 :contents-end 10586 :post-blank 0 :parent #363) #("PACKAGE" 0 7 (:parent #367))) (subscript (:begin 10586 :end 10591 :use-brackets-p nil :contents-begin 10587 :contents-end 10591 :post-blank 0 :parent #363) #("PATH" 0 4 (:parent #368))) #("=../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 #363))) (paragraph (:begin 11018 :end 11222 :contents-begin 11018 :contents-end 11221 :post-blank 1 :post-affiliated 11018 :mode nil :granularity nil :parent #355) #("/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 #364))) (paragraph (:begin 11222 :end 15256 :contents-begin 11222 :contents-end 15256 :post-blank 0 :post-affiliated 11222 :mode nil :granularity nil :parent #355) #(" which should have the same HASH values " 0 48 (:parent #365)) (italic (:begin 11270 :end 12179 :post-blank 0 :contents-begin 11271 :contents-end 12178 :parent #365) #("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 #369))) #(".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 #365)) (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 12979 :end 13044 :contents-begin nil :contents-end nil :post-blank 0 :parent #365)) #("\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 #365)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13292 :end 13325 :contents-begin nil :contents-end nil :post-blank 1 :parent #365)) #("--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 #365)) (subscript (:begin 13549 :end 13557 :use-brackets-p nil :contents-begin 13550 :contents-end 13557 :post-blank 0 :parent #365) #("PACKAGE" 0 7 (:parent #375))) (subscript (:begin 13557 :end 13562 :use-brackets-p nil :contents-begin 13558 :contents-end 13562 :post-blank 0 :parent #365) #("PATH" 0 4 (:parent #376))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #365)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13678 :end 13705 :contents-begin nil :contents-end nil :post-blank 0 :parent #365)) #("\"\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 #365)) (subscript (:begin 14275 :end 14283 :use-brackets-p nil :contents-begin 14276 :contents-end 14283 :post-blank 0 :parent #365) #("PACKAGE" 0 7 (:parent #380))) (subscript (:begin 14283 :end 14288 :use-brackets-p nil :contents-begin 14284 :contents-end 14288 :post-blank 0 :parent #365) #("PATH" 0 4 (:parent #381))) #("=../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 #365)) (subscript (:begin 14947 :end 14955 :use-brackets-p nil :contents-begin 14948 :contents-end 14955 :post-blank 0 :parent #365) #("PACKAGE" 0 7 (:parent #383))) (subscript (:begin 14955 :end 14960 :use-brackets-p nil :contents-begin 14956 :contents-end 14960 :post-blank 0 :parent #365) #("PATH" 0 4 (:parent #384))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #365)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 15074 :end 15106 :contents-begin nil :contents-end nil :post-blank 0 :parent #365)) #("\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" 0 150 (:parent #365)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #))
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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 "Running Redis" :begin 2849 :end 2931 :pre-blank 1 :contents-begin 2866 :contents-end 2930 :robust-begin 2868 :robust-end 2928 :level 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 (#("Running Redis" 0 13 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2866 :end 2931 :contents-begin 2866 :contents-end 2930 :robust-begin 2866 :robust-end 2928 :post-blank 1 :post-affiliated 2866 :mode section :granularity nil :parent #180) (paragraph (:begin 2866 :end 2913 :contents-begin 2866 :contents-end 2912 :post-blank 1 :post-affiliated 2866 :mode planning :granularity nil :parent #183) #("Install redis. Make sure you add the setting:\n" 0 46 (:parent #186))) (fixed-width (:begin 2913 :end 2930 :value "appendonly yes" :post-blank 1 :post-affiliated 2913 :mode nil :granularity nil :parent #183)))) (headline (:raw-value "Run MariaDB server" :begin 2931 :end 5782 :pre-blank 0 :contents-begin 2952 :contents-end 5781 :robust-begin 2954 :robust-end 5779 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2931 :title (#("Run MariaDB server" 0 18 (:parent #181))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 2952 :end 4250 :pre-blank 1 :contents-begin 2986 :contents-end 4249 :robust-begin 2988 :robust-end 4247 :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 2952 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #184))) :mode section :granularity nil :parent #181) (section (:begin 2986 :end 4250 :contents-begin 2986 :contents-end 4249 :robust-begin 2986 :robust-end 4247 :post-blank 1 :post-affiliated 2986 :mode section :granularity nil :parent #184) (paragraph (:begin 2986 :end 3015 :contents-begin 2986 :contents-end 3014 :post-blank 1 :post-affiliated 2986 :mode planning :granularity nil :parent #187) (italic (:begin 2986 :end 3013 :post-blank 0 :contents-begin 2987 :contents-end 3012 :parent #190) #("Note: we moved to MariaDB" 0 25 (:parent #193))) #("\n" 0 1 (:parent #190))) (paragraph (:begin 3015 :end 3152 :contents-begin 3015 :contents-end 3151 :post-blank 1 :post-affiliated 3015 :mode nil :granularity nil :parent #187) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #191))) (paragraph (:begin 3152 :end 3179 :contents-begin 3152 :contents-end 3178 :post-blank 1 :post-affiliated 3152 :mode nil :granularity nil :parent #187) #("As root configure and run\n" 0 26 (:parent #192))) (src-block (:language "bash" :switches nil :parameters nil :begin 3179 :end 3475 :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 3179 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3475 :end 3523 :contents-begin 3475 :contents-end 3522 :post-blank 1 :post-affiliated 3475 :mode nil :granularity nil :parent #187) #("If you want to run as root you may have to set\n" 0 47 (:parent #194))) (fixed-width (:begin 3523 :end 3563 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 3523 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3563 :end 3585 :contents-begin 3563 :contents-end 3584 :post-blank 1 :post-affiliated 3563 :mode nil :granularity nil :parent #187) #("You also need to set\n" 0 21 (:parent #196))) (fixed-width (:begin 3585 :end 3608 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 3585 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3608 :end 3688 :contents-begin 3608 :contents-end 3687 :post-blank 1 :post-affiliated 3608 :mode nil :granularity nil :parent #187) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #198))) (paragraph (:begin 3688 :end 3757 :contents-begin 3688 :contents-end 3756 :post-blank 1 :post-affiliated 3688 :mode nil :granularity nil :parent #187) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #199))) (fixed-width (:begin 3757 :end 3872 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 3757 :mode nil :granularity nil :parent #187)) (paragraph (:begin 3872 :end 3950 :contents-begin 3872 :contents-end 3949 :post-blank 1 :post-affiliated 3872 :mode nil :granularity nil :parent #187) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #201))) (fixed-width (:begin 3950 :end 4060 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 3950 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4060 :end 4087 :contents-begin 4060 :contents-end 4086 :post-blank 1 :post-affiliated 4060 :mode nil :granularity nil :parent #187) #("When you get errors like:\n" 0 26 (:parent #203))) (fixed-width (:begin 4087 :end 4201 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4087 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4201 :end 4222 :contents-begin 4201 :contents-end 4221 :post-blank 1 :post-affiliated 4201 :mode nil :granularity nil :parent #187) #("you may need to set\n" 0 20 (:parent #205))) (fixed-width (:begin 4222 :end 4249 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4222 :mode nil :granularity nil :parent #187)))) (headline (:raw-value "Load the small database in MySQL" :begin 4250 :end 5782 :pre-blank 1 :contents-begin 4287 :contents-end 5781 :robust-begin 4289 :robust-end 5779 :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 4250 :title (#("Load the small database in MySQL" 0 32 (:parent #185))) :mode nil :granularity nil :parent #181) (section (:begin 4287 :end 5782 :contents-begin 4287 :contents-end 5781 :robust-begin 4287 :robust-end 5779 :post-blank 1 :post-affiliated 4287 :mode section :granularity nil :parent #185) (paragraph (:begin 4287 :end 4594 :contents-begin 4287 :contents-end 4593 :post-blank 1 :post-affiliated 4287 :mode planning :granularity nil :parent #188) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #191)) (subscript (:begin 4450 :end 4457 :use-brackets-p nil :contents-begin 4451 :contents-end 4457 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #195))) (subscript (:begin 4457 :end 4459 :use-brackets-p nil :contents-begin 4458 :contents-end 4459 :post-blank 0 :parent #191) #("s" 0 1 (:parent #196))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #191)) (subscript (:begin 4535 :end 4542 :use-brackets-p nil :contents-begin 4536 :contents-end 4542 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 4542 :end 4548 :use-brackets-p nil :contents-begin 4543 :contents-end 4548 :post-blank 0 :parent #191) #("plant" 0 5 (:parent #199))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #191))) (paragraph (:begin 4594 :end 4622 :contents-begin 4594 :contents-end 4621 :post-blank 1 :post-affiliated 4594 :mode nil :granularity nil :parent #188) #("Download one database from\n" 0 27 (:parent #192))) (paragraph (:begin 4622 :end 4670 :contents-begin 4622 :contents-end 4669 :post-blank 1 :post-affiliated 4622 :mode nil :granularity nil :parent #188) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4622 :end 4668 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4670 :end 4729 :contents-begin 4670 :contents-end 4728 :post-blank 1 :post-affiliated 4670 :mode nil :granularity nil :parent #188) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4670 :end 4727 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 4729 :end 4748 :contents-begin 4729 :contents-end 4747 :post-blank 1 :post-affiliated 4729 :mode nil :granularity nil :parent #188) #("Check the md5sum.\n" 0 18 (:parent #195))) (paragraph (:begin 4748 :end 4819 :contents-begin 4748 :contents-end 4818 :post-blank 1 :post-affiliated 4748 :mode nil :granularity nil :parent #188) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #196))) (fixed-width (:begin 4819 :end 4920 :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 4819 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4920 :end 4967 :contents-begin 4920 :contents-end 4966 :post-blank 1 :post-affiliated 4920 :mode nil :granularity nil :parent #188) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #198))) (fixed-width (:begin 4967 :end 4984 :value "myslq -u root" :post-blank 2 :post-affiliated 4967 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4984 :end 4989 :contents-begin 4984 :contents-end 4988 :post-blank 1 :post-affiliated 4984 :mode nil :granularity nil :parent #188) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 4989 :end 5215 :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 4989 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5215 :end 5280 :contents-begin 5215 :contents-end 5279 :post-blank 1 :post-affiliated 5215 :mode nil :granularity nil :parent #188) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 5280 :end 5379 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5280 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5379 :end 5486 :contents-begin 5379 :contents-end 5485 :post-blank 1 :post-affiliated 5379 :mode nil :granularity nil :parent #188) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 5486 :end 5649 :contents-begin 5486 :contents-end 5648 :post-blank 1 :post-affiliated 5486 :mode nil :granularity nil :parent #188) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 5649 :end 5781 :contents-begin 5649 :contents-end 5781 :post-blank 0 :post-affiliated 5649 :mode nil :granularity nil :parent #188) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript (:begin 5700 :end 5707 :use-brackets-p nil :contents-begin 5701 :contents-end 5707 :post-blank 0 :parent #206) #("webqtl" 0 6 (:parent #210))) (subscript (:begin 5707 :end 5709 :use-brackets-p nil :contents-begin 5708 :contents-end 5709 :post-blank 0 :parent #206) #("s" 0 1 (:parent #211))) #(", or\nchange the settings in etc/default" 0 39 (:parent #206)) (subscript (:begin 5748 :end 5761 :use-brackets-p nil :contents-begin 5749 :contents-end 5760 :post-blank 1 :parent #206) #("settings.py" 0 11 (:parent #213))) #("to match your path.\n" 0 20 (:parent #206)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5782 :end 5946 :pre-blank 1 :contents-begin 5806 :contents-end 5945 :robust-begin 5808 :robust-end 5943 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5782 :title (#("GN2 Dependency Graph" 0 20 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5806 :end 5946 :contents-begin 5806 :contents-end 5945 :robust-begin 5806 :robust-end 5943 :post-blank 1 :post-affiliated 5806 :mode section :granularity nil :parent #182) (paragraph (:begin 5806 :end 5867 :contents-begin 5806 :contents-end 5866 :post-blank 1 :post-affiliated 5806 :mode planning :granularity nil :parent #185) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #188))) (paragraph (:begin 5867 :end 5945 :contents-begin 5897 :contents-end 5945 :post-blank 0 :post-affiliated 5897 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #185) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 5897 :end 5944 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))))) (headline (:raw-value "Working with the GN2 source code" :begin 5946 :end 6008 :pre-blank 1 :contents-begin 5982 :contents-end 6007 :robust-begin 5984 :robust-end 6005 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5946 :title (#("Working with the GN2 source code" 0 32 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 5982 :end 6008 :contents-begin 5982 :contents-end 6007 :robust-begin 5982 :robust-end 6005 :post-blank 1 :post-affiliated 5982 :mode section :granularity nil :parent #183) (paragraph (:begin 5982 :end 6007 :contents-begin 5982 :contents-end 6007 :post-blank 0 :post-affiliated 5982 :mode planning :granularity nil :parent #186) #("See " 0 4 (:parent #189)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 5986 :end 6005 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "Read more" :begin 6008 :end 6158 :pre-blank 1 :contents-begin 6021 :contents-end 6157 :robust-begin 6023 :robust-end 6155 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6008 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 6021 :end 6158 :contents-begin 6021 :contents-end 6157 :robust-begin 6021 :robust-end 6155 :post-blank 1 :post-affiliated 6021 :mode section :granularity nil :parent #184) (paragraph (:begin 6021 :end 6157 :contents-begin 6021 :contents-end 6157 :post-blank 0 :post-affiliated 6021 :mode planning :granularity nil :parent #187) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #190)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6076 :end 6096 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #190))))) (headline (:raw-value "Trouble shooting" :begin 6158 :end 8609 :pre-blank 1 :contents-begin 6178 :contents-end 8607 :robust-begin 6180 :robust-end 8605 :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 6158 :title (#("Trouble shooting" 0 16 (:parent #185))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6178 :end 6712 :pre-blank 1 :contents-begin 6218 :contents-end 6712 :robust-begin 6220 :robust-end 6710 :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 6178 :title (#("ImportError: No module named jinja2" 0 35 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 6218 :end 6712 :contents-begin 6218 :contents-end 6712 :robust-begin 6218 :robust-end 6710 :post-blank 0 :post-affiliated 6218 :mode section :granularity nil :parent #188) (paragraph (:begin 6218 :end 6453 :contents-begin 6218 :contents-end 6452 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #191) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #194)) (subscript (:begin 6385 :end 6391 :use-brackets-p nil :contents-begin 6386 :contents-end 6390 :post-blank 1 :parent #194) #("PATH" 0 4 (:parent #198))) #("and R" 0 5 (:parent #194)) (subscript (:begin 6396 :end 6401 :use-brackets-p nil :contents-begin 6397 :contents-end 6401 :post-blank 0 :parent #194) #("LIBS" 0 4 (:parent #200))) (subscript (:begin 6401 :end 6407 :use-brackets-p nil :contents-begin 6402 :contents-end 6406 :post-blank 1 :parent #194) #("SITE" 0 4 (:parent #201))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #194))) (fixed-width (:begin 6453 :end 6484 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6453 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6484 :end 6500 :contents-begin 6484 :contents-end 6499 :post-blank 1 :post-affiliated 6484 :mode nil :granularity nil :parent #191) #("On one system:\n" 0 15 (:parent #196))) (fixed-width (:begin 6500 :end 6688 :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 6500 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6688 :end 6712 :contents-begin 6688 :contents-end 6712 :post-blank 0 :post-affiliated 6688 :mode nil :granularity nil :parent #191) #("and perhaps a few more.\n" 0 24 (:parent #198))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 6712 :end 7208 :pre-blank 1 :contents-begin 6821 :contents-end 7207 :robust-begin 6823 :robust-end 7205 :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 6712 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #189)) (subscript (:begin 6755 :end 6760 :use-brackets-p nil :contents-begin 6756 :contents-end 6760 :post-blank 0 :parent #189) #("data" 0 4 (:parent #231))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #189)) (subscript (:begin 6803 :end 6809 :use-brackets-p nil :contents-begin 6804 :contents-end 6809 :post-blank 0 :parent #189) #("files" 0 5 (:parent #233))) #("/genotype'" 0 10 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 6821 :end 7208 :contents-begin 6821 :contents-end 7207 :robust-begin 6821 :robust-end 7205 :post-blank 1 :post-affiliated 6821 :mode section :granularity nil :parent #189) (paragraph (:begin 6821 :end 7043 :contents-begin 6821 :contents-end 7042 :post-blank 1 :post-affiliated 6821 :mode planning :granularity nil :parent #192) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #195)) (subscript (:begin 6870 :end 6875 :use-brackets-p nil :contents-begin 6871 :contents-end 6875 :post-blank 0 :parent #195) #("data" 0 4 (:parent #199))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #195)) (subscript (:begin 6999 :end 7012 :use-brackets-p nil :contents-begin 7000 :contents-end 7011 :post-blank 1 :parent #195) #("settings.py" 0 11 (:parent #201))) #("(see above in\nthis document).\n" 0 30 (:parent #195))) (paragraph (:begin 7043 :end 7117 :contents-begin 7043 :contents-end 7116 :post-blank 1 :post-affiliated 7043 :mode nil :granularity nil :parent #192) #("You can use the GENENETWORK" 0 27 (:parent #196)) (subscript (:begin 7070 :end 7077 :use-brackets-p nil :contents-begin 7071 :contents-end 7076 :post-blank 1 :parent #196) #("FILES" 0 5 (:parent #200))) #("switch to set the datadir, for example\n" 0 39 (:parent #196))) (fixed-width (:begin 7117 :end 7207 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7117 :mode nil :granularity nil :parent #192)))) (headline (:raw-value "Can't run a module" :begin 7208 :end 7442 :pre-blank 1 :contents-begin 7231 :contents-end 7442 :robust-begin 7233 :robust-end 7440 :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 7208 :title (#("Can't run a module" 0 18 (:parent #190))) :mode nil :granularity nil :parent #185) (section (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :robust-begin 7231 :robust-end 7440 :post-blank 0 :post-affiliated 7231 :mode section :granularity nil :parent #190) (paragraph (:begin 7231 :end 7442 :contents-begin 7231 :contents-end 7442 :post-blank 0 :post-affiliated 7231 :mode planning :granularity nil :parent #193) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #196))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7442 :end 7943 :pre-blank 1 :contents-begin 7474 :contents-end 7942 :robust-begin 7476 :robust-end 7940 :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 7442 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #191))) :mode nil :granularity nil :parent #185) (section (:begin 7474 :end 7943 :contents-begin 7474 :contents-end 7942 :robust-begin 7474 :robust-end 7940 :post-blank 1 :post-affiliated 7474 :mode section :granularity nil :parent #191) (paragraph (:begin 7474 :end 7486 :contents-begin 7474 :contents-end 7485 :post-blank 1 :post-affiliated 7474 :mode planning :granularity nil :parent #194) #("This error\n" 0 11 (:parent #197))) (fixed-width (:begin 7486 :end 7566 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7486 :mode nil :granularity nil :parent #194)) (paragraph (:begin 7566 :end 7697 :contents-begin 7566 :contents-end 7696 :post-blank 1 :post-affiliated 7566 :mode nil :granularity nil :parent #194) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #199))) (paragraph (:begin 7697 :end 7942 :contents-begin 7697 :contents-end 7942 :post-blank 0 :post-affiliated 7697 :mode nil :granularity nil :parent #194) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #200)) (subscript (:begin 7760 :end 7765 :use-brackets-p nil :contents-begin 7761 :contents-end 7765 :post-blank 0 :parent #200) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 7765 :end 7770 :use-brackets-p nil :contents-begin 7766 :contents-end 7770 :post-blank 0 :parent #200) #("SITE" 0 4 (:parent #205))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #200))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7943 :end 8609 :pre-blank 1 :contents-begin 7995 :contents-end 8607 :robust-begin 7997 :robust-end 8605 :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 7943 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #192))) :mode nil :granularity nil :parent #185) (section (:begin 7995 :end 8609 :contents-begin 7995 :contents-end 8607 :robust-begin 7995 :robust-end 8605 :post-blank 2 :post-affiliated 7995 :mode section :granularity nil :parent #192) (paragraph (:begin 7995 :end 8016 :contents-begin 7995 :contents-end 8015 :post-blank 1 :post-affiliated 7995 :mode planning :granularity nil :parent #195) #("The following error\n" 0 20 (:parent #198))) (fixed-width (:begin 8016 :end 8211 :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 8016 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8211 :end 8369 :contents-begin 8211 :contents-end 8368 :post-blank 1 :post-affiliated 8211 :mode nil :granularity nil :parent #195) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #200))) (fixed-width (:begin 8369 :end 8391 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8369 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8391 :end 8448 :contents-begin 8391 :contents-end 8447 :post-blank 1 :post-affiliated 8391 :mode nil :granularity nil :parent #195) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #202))) (fixed-width (:begin 8448 :end 8470 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8448 :mode nil :granularity nil :parent #195)) (paragraph (:begin 8470 :end 8541 :contents-begin 8470 :contents-end 8540 :post-blank 1 :post-affiliated 8470 :mode nil :granularity nil :parent #195) #("if that works run genenetwork after setting SQL" 0 47 (:parent #204)) (subscript (:begin 8517 :end 8522 :use-brackets-p nil :contents-begin 8518 :contents-end 8521 :post-blank 1 :parent #204) #("URI" 0 3 (:parent #208))) #("to something like\n" 0 18 (:parent #204))) (fixed-width (:begin 8541 :end 8607 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8541 :mode nil :granularity nil :parent #195))))) (headline (:raw-value "IRC session" :begin 8609 :end 15256 :pre-blank 1 :contents-begin 8624 :contents-end 15256 :robust-begin 8626 :robust-end 15254 :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 8609 :title (#("IRC session" 0 11 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 8624 :end 15256 :contents-begin 8624 :contents-end 15256 :robust-begin 8624 :robust-end 15254 :post-blank 0 :post-affiliated 8624 :mode section :granularity nil :parent #186) (paragraph (:begin 8624 :end 8733 :contents-begin 8624 :contents-end 8732 :post-blank 1 :post-affiliated 8624 :mode planning :granularity nil :parent #189) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #192))) (paragraph (:begin 8733 :end 9294 :contents-begin 8733 :contents-end 9293 :post-blank 1 :post-affiliated 8733 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 8740 :end 8744 :use-brackets-p nil :contents-begin 8741 :contents-end 8744 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #193))) (paragraph (:begin 9294 :end 9384 :contents-begin 9294 :contents-end 9383 :post-blank 1 :post-affiliated 9294 :mode nil :granularity nil :parent #189) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 9384 :end 9529 :contents-begin 9384 :contents-end 9528 :post-blank 1 :post-affiliated 9384 :mode nil :granularity nil :parent #189) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 9414 :end 9422 :use-brackets-p nil :contents-begin 9415 :contents-end 9422 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 9422 :end 9427 :use-brackets-p nil :contents-begin 9423 :contents-end 9427 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 9529 :end 9825 :contents-begin 9529 :contents-end 9824 :post-blank 1 :post-affiliated 9529 :mode nil :granularity nil :parent #189) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #196))) (paragraph (:begin 9825 :end 11018 :contents-begin 9825 :contents-end 11017 :post-blank 1 :post-affiliated 9825 :mode nil :granularity nil :parent #189) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #197)) (subscript (:begin 10578 :end 10586 :use-brackets-p nil :contents-begin 10579 :contents-end 10586 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 10586 :end 10591 :use-brackets-p nil :contents-begin 10587 :contents-end 10591 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #197))) (paragraph (:begin 11018 :end 11222 :contents-begin 11018 :contents-end 11221 :post-blank 1 :post-affiliated 11018 :mode nil :granularity nil :parent #189) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #198))) (paragraph (:begin 11222 :end 15256 :contents-begin 11222 :contents-end 15256 :post-blank 0 :post-affiliated 11222 :mode nil :granularity nil :parent #189) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 11270 :end 12179 :post-blank 0 :contents-begin 11271 :contents-end 12178 :parent #199) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n
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