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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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #178) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #181) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #184))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #192) #("Redis\n" 0 6 (:parent #195)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #193) #("Mariadb\n" 0 8 (:parent #196))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #179) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #182) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #185)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #185)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #185))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #182)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #180) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #183) #("We run a GNU Guix channel with packages at " 0 43 (:parent #186)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #186) #("guix-bioinformatics" 0 19 (:parent #190))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #186)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #186) #("PACKAGE" 0 7 (:parent #192))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #186) #("PATH" 0 4 (:parent #193))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #186))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #183) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #188))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #183) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #190))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #183) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #192))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #183) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #194)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #194) #("substitutes" 0 11 (:parent #198))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #194)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\"` switch.\n" 0 11 (:parent #194))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #183) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #195))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #183) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #197))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #181) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #184) #("Check out the source with git:\n" 0 31 (:parent #187))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #184) #("Run GN2 with above Guix profile\n" 0 32 (:parent #189))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #184) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #191))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #184) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #192))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #184) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #193))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #184) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #194))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #184) #("And browse on your local machine to " 0 36 (:parent #195)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #("\n" 0 1 (:parent #195))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #182) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #185) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #188)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #188) #("README" 0 6 (:parent #192))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #188))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #183) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #186) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #189))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #184))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #187))) :mode section :granularity nil :parent #184) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #187) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #190) #("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 #193))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #190) #("As root configure the Guix profile\n" 0 35 (:parent #194))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #190) #("and run for example\n" 0 20 (:parent #196))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #190) #("If you want to run as root you may have to set\n" 0 47 (:parent #198))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #190) #("You also need to set\n" 0 21 (:parent #200))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #190) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #202))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #190) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #203))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #190) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #205))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #190) #("When you get errors like:\n" 0 26 (:parent #207))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #190) #("you may need to set\n" 0 20 (:parent #209))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #190)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #188))) :mode nil :granularity nil :parent #184) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #188) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #191) #("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 #194)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #194) #("s" 0 1 (:parent #199))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #194)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #201))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #194) #("plant" 0 5 (:parent #202))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #194))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #191) #("Download one database from\n" 0 27 (:parent #195))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #191) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #191) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #197))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #191) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #199))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #191)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #191) #("and\n" 0 4 (:parent #202))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #191) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #204))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #191) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #206))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #191) #("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 #207))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #191) #("Note for the plant database you can rename it to db" 0 51 (:parent #208)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #208) #("webqtl" 0 6 (:parent #212))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #208) #("s" 0 1 (:parent #213))) #(", or\nchange the settings in etc/default" 0 39 (:parent #208)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #208) #("settings.py" 0 11 (:parent #215))) #("to match your path.\n" 0 20 (:parent #208)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #185) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #188) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #191)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #("\n" 0 1 (:parent #191))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #186) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #189) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #192))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #189) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #187))) :mode nil :granularity nil :parent #172) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #187) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #190) #("See " 0 4 (:parent #193)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #(".\n" 0 2 (:parent #193))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #188))) :mode nil :granularity nil :parent #172) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #188) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #191) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #194)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #194))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #189))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #192))) :mode section :granularity nil :parent #189) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #192) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #195) #("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 #198)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #198) #("PATH" 0 4 (:parent #202))) #("and R" 0 5 (:parent #198)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #198) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #198) #("SITE" 0 4 (:parent #205))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #198))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #195) #("On one system:\n" 0 15 (:parent #200))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #195) #("and perhaps a few more.\n" 0 24 (:parent #202))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #193)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #193) #("data" 0 4 (:parent #235))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #193)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #193) #("files" 0 5 (:parent #237))) #("/genotype'" 0 10 (:parent #193))) :mode nil :granularity nil :parent #189) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #193) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #196) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #199)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #199) #("data" 0 4 (:parent #203))) #(". 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 #199)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #199) #("settings.py" 0 11 (:parent #205))) #("(see above in\nthis document).\n" 0 30 (:parent #199))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #196) #("You can use the GENENETWORK" 0 27 (:parent #200)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #200) #("FILES" 0 5 (:parent #204))) #("switch to set the datadir, for example\n" 0 39 (:parent #200))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #196)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #194))) :mode nil :granularity nil :parent #189) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #194) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #197) #("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 #200))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #195))) :mode nil :granularity nil :parent #189) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #195) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #198) #("This error\n" 0 11 (:parent #201))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #198)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #198) #("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 #203))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #198) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #204)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #204) #("LIBS" 0 4 (:parent #208))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #204) #("SITE" 0 4 (:parent #209))) #(". 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 #204))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #196))) :mode nil :granularity nil :parent #189) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #196) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #199) #("The following error\n" 0 20 (:parent #202))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #199)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #199) #("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 #204))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #199) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #206))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #199) #("if that works run genenetwork after setting SQL" 0 47 (:parent #208)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #208) #("URI" 0 3 (:parent #212))) #("to something like\n" 0 18 (:parent #208))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #199))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #190))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #193))) :mode section :granularity nil :parent #190) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #193) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #196) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #199))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #196) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #200) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #203) #("Base install\n" 0 13 (:parent #206))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #203) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #210) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #213)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #211) #("Get Guix build going\n" 0 21 (:parent #214))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #211) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #218) #("Build the correct version of Guix\n" 0 34 (:parent #221)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #219) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #222)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #222)) #("\n" 0 1 (:parent #222)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #220) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #223)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #212) #("Create a gn2 user and home with space\n" 0 38 (:parent #215)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #213) #("Install redis\n" 0 14 (:parent #216))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #213) (item (:bullet "- " :begin 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #343) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 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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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #386) #("add to systemd\n" 0 15 (:parent #389)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #178) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #181) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #184))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Debian-derived distros\nmay support\n" 0 117 (:parent #185))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #182)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #180) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #183) #("We run a GNU Guix channel with packages at " 0 43 (:parent #186)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #186) #("guix-bioinformatics" 0 19 (:parent #190))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #186)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #186) #("PACKAGE" 0 7 (:parent #192))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #186) #("PATH" 0 4 (:parent #193))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #186))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #183) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #188))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #183) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #190))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #183) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #192))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #183) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #194)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #194) #("substitutes" 0 11 (:parent #198))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #194)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\"` switch.\n" 0 11 (:parent #194))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #183) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #195))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #183) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #197))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #181) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #184) #("Check out the source with git:\n" 0 31 (:parent #187))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #184) #("Run GN2 with above Guix profile\n" 0 32 (:parent #189))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #184) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #191))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #184) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #192))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #184) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #193))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #184) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #194))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #184) #("And browse on your local machine to " 0 36 (:parent #195)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #("\n" 0 1 (:parent #195))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #182) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #185) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #188)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #188) #("README" 0 6 (:parent #192))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #188))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #183) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #186) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #189))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #184))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #187))) :mode section :granularity nil :parent #184) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #187) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #190) #("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 #193))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #190) #("As root configure the Guix profile\n" 0 35 (:parent #194))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #190) #("and run for example\n" 0 20 (:parent #196))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #190) #("If you want to run as root you may have to set\n" 0 47 (:parent #198))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #190) #("You also need to set\n" 0 21 (:parent #200))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #190) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #202))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #190) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #203))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #190) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #205))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #190) #("When you get errors like:\n" 0 26 (:parent #207))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #190) #("you may need to set\n" 0 20 (:parent #209))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #190)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #188))) :mode nil :granularity nil :parent #184) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #188) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #191) #("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 #194)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #194) #("s" 0 1 (:parent #199))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #194)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #201))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #194) #("plant" 0 5 (:parent #202))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #194))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #191) #("Download one database from\n" 0 27 (:parent #195))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #191) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #191) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #197))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #191) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #199))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #191)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #191) #("and\n" 0 4 (:parent #202))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #191) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #204))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #191) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #206))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #191) #("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 #207))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #191) #("Note for the plant database you can rename it to db" 0 51 (:parent #208)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #208) #("webqtl" 0 6 (:parent #212))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #208) #("s" 0 1 (:parent #213))) #(", or\nchange the settings in etc/default" 0 39 (:parent #208)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #208) #("settings.py" 0 11 (:parent #215))) #("to match your path.\n" 0 20 (:parent #208)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #185) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #188) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #191)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #("\n" 0 1 (:parent #191))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #186) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #189) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #192))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #189) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #187))) :mode nil :granularity nil :parent #172) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #187) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #190) #("See " 0 4 (:parent #193)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #(".\n" 0 2 (:parent #193))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #188))) :mode nil :granularity nil :parent #172) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #188) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #191) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #194)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #194))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #189))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #192))) :mode section :granularity nil :parent #189) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #192) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #195) #("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 #198)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #198) #("PATH" 0 4 (:parent #202))) #("and R" 0 5 (:parent #198)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #198) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #198) #("SITE" 0 4 (:parent #205))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #198))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #195) #("On one system:\n" 0 15 (:parent #200))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #195) #("and perhaps a few more.\n" 0 24 (:parent #202))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #193)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #193) #("data" 0 4 (:parent #235))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #193)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #193) #("files" 0 5 (:parent #237))) #("/genotype'" 0 10 (:parent #193))) :mode nil :granularity nil :parent #189) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #193) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #196) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #199)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #199) #("data" 0 4 (:parent #203))) #(". 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 #199)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #199) #("settings.py" 0 11 (:parent #205))) #("(see above in\nthis document).\n" 0 30 (:parent #199))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #196) #("You can use the GENENETWORK" 0 27 (:parent #200)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #200) #("FILES" 0 5 (:parent #204))) #("switch to set the datadir, for example\n" 0 39 (:parent #200))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #196)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #194))) :mode nil :granularity nil :parent #189) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #194) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #197) #("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 #200))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #195))) :mode nil :granularity nil :parent #189) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #195) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #198) #("This error\n" 0 11 (:parent #201))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #198)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #198) #("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 #203))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #198) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #204)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #204) #("LIBS" 0 4 (:parent #208))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #204) #("SITE" 0 4 (:parent #209))) #(". 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 #204))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #196))) :mode nil :granularity nil :parent #189) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #196) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #199) #("The following error\n" 0 20 (:parent #202))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #199)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #199) #("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 #204))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #199) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #206))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #199) #("if that works run genenetwork after setting SQL" 0 47 (:parent #208)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #208) #("URI" 0 3 (:parent #212))) #("to something like\n" 0 18 (:parent #208))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #199))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #190))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #193))) :mode section :granularity nil :parent #190) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #193) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #196) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #199))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #219) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #222)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #222)) #("\n" 0 1 (:parent #222)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #212) #("Create a gn2 user and home with space\n" 0 38 (:parent #215)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#213) #("Install redis\n" 0 14 (:parent #216))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #213) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #220) #("add to systemd\n" 0 15 (:parent #223)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #217) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #221) #("update redis.cnf\n" 0 17 (:parent #224)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #217) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #222) #("update database\n" 0 16 (:parent #225)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #184) #("Guix-notes" 0 10 (:parent #190))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #184))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #181) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #185) #("Guix bioinformatics" 0 19 (:parent #189))) #("and " 0 4 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #185) #("GNU Guix" 0 8 (:parent #191))) #(".\n" 0 2 (:parent #185))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #181) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #186)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #186) #("GN2 Dependency Graph" 0 20 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #179))) :mode nil :granularity nil :parent #173) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #179) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #182) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #185))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #182) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #189) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #192)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #190) #("A path to the (static) genotype files\n" 0 38 (:parent #193)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #191) #("Gn-proxy for authentication\n" 0 28 (:parent #194)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #192) #("The genenetwork3 service\n" 0 25 (:parent #195)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #193) #("Redis\n" 0 6 (:parent #196)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #194) #("Mariadb\n" 0 8 (:parent #197))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #180))) :mode nil :granularity nil :parent #173) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #180) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #183) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #186)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #186)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #186))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #183)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #181))) :mode nil :granularity nil :parent #173) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #181) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #184) #("We run a GNU Guix channel with packages at " 0 43 (:parent #187)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #187) #("guix-bioinformatics" 0 19 (:parent #191))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #187)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #187) #("PACKAGE" 0 7 (:parent #193))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #187) #("PATH" 0 4 (:parent #194))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #187))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #184)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #184) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #189))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #184)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #184) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #191))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #184)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #184) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #193))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #184)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #184) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #195)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #195) #("substitutes" 0 11 (:parent #199))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #195)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #195)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #195)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #("\"` switch.\n" 0 11 (:parent #195))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #184) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #196))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #184)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #184) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #198))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #182))) :mode nil :granularity nil :parent #173) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #182) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #185) #("Check out the source with git:\n" 0 31 (:parent #188))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #185)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #185) #("Run GN2 with above Guix profile\n" 0 32 (:parent #190))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #185)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #185) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #192))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #185) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #193))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #185) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #194))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #185) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #195))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #185) #("And browse on your local machine to " 0 36 (:parent #196)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #183))) :mode nil :granularity nil :parent #173) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #183) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #186) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #189)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #189) #("README" 0 6 (:parent #193))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #189))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #184))) :mode nil :granularity nil :parent #173) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #184) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #187) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #190))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #185))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #188) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #191) #("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 #194))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #191) #("As root configure the Guix profile\n" 0 35 (:parent #195))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #191) #("and run for example\n" 0 20 (:parent #197))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #191)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #191) #("If you want to run as root you may have to set\n" 0 47 (:parent #199))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #191)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #191) #("You also need to set\n" 0 21 (:parent #201))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #191)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #191) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #203))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #191) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #204))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #191)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #191) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #206))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #191)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #191) #("When you get errors like:\n" 0 26 (:parent #208))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #191)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #191) #("you may need to set\n" 0 20 (:parent #210))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #191)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #189) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #192) #("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 #195)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #195) #("webqtl" 0 6 (:parent #199))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #195) #("s" 0 1 (:parent #200))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #195)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #195) #("webqtl" 0 6 (:parent #202))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #195) #("plant" 0 5 (:parent #203))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #195))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #192) #("Download one database from\n" 0 27 (:parent #196))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #192) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #197)) #("\n" 0 1 (:parent #197))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #192) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #198))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #192) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #200))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #192)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #192) #("and\n" 0 4 (:parent #203))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #192) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #205))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #192) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #207))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #192) #("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 #208))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #192) #("Note for the plant database you can rename it to db" 0 51 (:parent #209)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #209) #("webqtl" 0 6 (:parent #213))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #209) #("s" 0 1 (:parent #214))) #(", or\nchange the settings in etc/default" 0 39 (:parent #209)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #209) #("settings.py" 0 11 (:parent #216))) #("to match your path.\n" 0 20 (:parent #209)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #186))) :mode nil :granularity nil :parent #173) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #186) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #189) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #192)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #189)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #187))) :mode nil :granularity nil :parent #173) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #187) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #190) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #193))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #190) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #188))) :mode nil :granularity nil :parent #173) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #188) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #191) #("See " 0 4 (:parent #194)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #(".\n" 0 2 (:parent #194))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #189))) :mode nil :granularity nil :parent #173) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #189) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #192) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #195)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #195))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #190))) :mode nil :granularity nil :parent #173) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #193))) :mode section :granularity nil :parent #190) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #193) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #196) #("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 #199)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #199) #("PATH" 0 4 (:parent #203))) #("and R" 0 5 (:parent #199)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #199) #("LIBS" 0 4 (:parent #205))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #199) #("SITE" 0 4 (:parent #206))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #199))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #196)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #196) #("On one system:\n" 0 15 (:parent #201))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #196)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #196) #("and perhaps a few more.\n" 0 24 (:parent #203))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #194)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #194) #("data" 0 4 (:parent #236))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #194)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #194) #("files" 0 5 (:parent #238))) #("/genotype'" 0 10 (:parent #194))) :mode nil :granularity nil :parent #190) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #194) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #197) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #200)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #200) #("data" 0 4 (:parent #204))) #(". 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 #200)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #200) #("settings.py" 0 11 (:parent #206))) #("(see above in\nthis document).\n" 0 30 (:parent #200))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #197) #("You can use the GENENETWORK" 0 27 (:parent #201)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #201) #("FILES" 0 5 (:parent #205))) #("switch to set the datadir, for example\n" 0 39 (:parent #201))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #197)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #195))) :mode nil :granularity nil :parent #190) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #195) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #198) #("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 #201))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #196))) :mode nil :granularity nil :parent #190) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #196) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #199) #("This error\n" 0 11 (:parent #202))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #199)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #199) #("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 #204))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #199) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #205)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #205) #("LIBS" 0 4 (:parent #209))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #205) #("SITE" 0 4 (:parent #210))) #(". 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 #205))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #197))) :mode nil :granularity nil :parent #190) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #197) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #200) #("The following error\n" 0 20 (:parent #203))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #200)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #200) #("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 #205))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #200)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #200) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #207))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #200)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #200) #("if that works run genenetwork after setting SQL" 0 47 (:parent #209)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #209) #("URI" 0 3 (:parent #213))) #("to something like\n" 0 18 (:parent #209))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #200))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #191))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #194))) :mode section :granularity nil :parent #191) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #194) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #197) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #200))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #197) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #201) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #204) #("Base install\n" 0 13 (:parent #207))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #204) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #208) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #211) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #214)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #208) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #212) #("Get Guix build going\n" 0 21 (:parent #215))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #212) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #216) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #219) #("Build the correct version of Guix\n" 0 34 (:parent #222)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #216) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #220) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #223)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #223)) #("\n" 0 1 (:parent #223)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #216) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #221) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #224)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #208) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #213) #("Create a gn2 user and home with space\n" 0 38 (:parent #216)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #208) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #214) #("Install redis\n" 0 14 (:parent #217))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #214) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #218) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #221) #("add to systemd\n" 0 15 (:parent #224)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #218) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #222) #("update redis.cnf\n" 0 17 (:parent #225)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #218) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #223) #("update database\n" 0 16 (:parent #226)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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:contents-end 156 :post-blank 0 :post-affiliated 124 :mode nil :granularity nil :parent (item (:bullet "- " :begin 121 :end 156 :contents-begin 124 :contents-end 156 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 187) (187 1 "- " nil nil nil 246) (246 1 "- " nil nil nil 311) (311 1 "- " nil nil nil 344) (344 1 "- " nil nil nil 379) (379 1 "- " nil nil nil 408) (408 1 "- " nil nil nil 603) (455 3 "- " nil nil nil 526) (526 3 "- " nil nil nil 603) (603 1 "- " nil nil nil 650) (650 1 "- " nil nil nil 701) (701 1 "- " nil nil nil 776) (776 1 "- " nil nil nil 805) (805 1 "- " nil nil nil 1360) (848 3 "- " nil nil nil 930) (930 3 "- " nil nil nil 1141) (1141 3 "- " nil nil nil 1189) (1189 3 "- " nil nil nil 1254) (1254 3 "- " nil nil nil 1360) (1360 1 "- " nil nil nil 1438) (1381 3 "- " nil nil nil 1438)) :pre-blank 0 :post-blank 0 :post-affiliated 121 :tag nil :mode item :granularity nil :parent (plain-list (:type unordered :begin 121 :end 1438 :contents-begin 121 :contents-end 1438 :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 187) (187 1 "- " nil nil nil 246) (246 1 "- " nil nil nil 311) (311 1 "- " nil nil nil 344) (344 1 "- " nil nil nil 379) (379 1 "- " nil nil nil 408) (408 1 "- " nil nil nil 603) (455 3 "- " nil nil nil 526) (526 3 "- " nil nil nil 603) (603 1 "- " nil nil nil 650) (650 1 "- " nil nil nil 701) (701 1 "- " nil nil nil 776) (776 1 "- " nil nil nil 805) (805 1 "- " nil nil nil 1360) (848 3 "- " nil nil nil 930) (930 3 "- " nil nil nil 1141) (1141 3 "- " nil nil nil 1189) (1189 3 "- " nil nil nil 1254) (1254 3 "- " nil nil nil 1360) (1360 1 "- " nil nil nil 1438) (1381 3 "- " nil nil nil 1438)) :post-blank 0 :post-affiliated 121 :mode planning :granularity nil :parent (section (:begin 121 :end 1439 :contents-begin 121 :contents-end 1438 :robust-begin 121 :robust-end 1436 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1439 :pre-blank 0 :contents-begin 121 :contents-end 1438 :robust-begin 123 :robust-end 1436 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #105))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #151) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #154))) #105 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #156) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #159) #("Large system deployments can get very " 0 38 (:parent #162)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #162) #("complex" 0 7 (:parent #166))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #162) #("Guix-notes" 0 10 (:parent #168))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #162))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #159) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #163) #("Guix bioinformatics" 0 19 (:parent #167))) #("and " 0 4 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #163) #("GNU Guix" 0 8 (:parent #169))) #(".\n" 0 2 (:parent #163))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #159) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #164)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #164) #("GN2 Dependency Graph" 0 20 (:parent #168))) #(".\n" 0 2 (:parent #164))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #157) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #160) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #163))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #168) #("A path to the (static) genotype files\n" 0 38 (:parent #171)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #169) #("Gn-proxy for authentication\n" 0 28 (:parent #172)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #170) #("The genenetwork3 service\n" 0 25 (:parent #173)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #171) #("Redis\n" 0 6 (:parent #174)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #172) #("Mariadb\n" 0 8 (:parent #175))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #158) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #161) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #164)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #164)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #164))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #161)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #159))) :mode nil :granularity nil :parent #151) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #159) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #162) #("We run a GNU Guix channel with packages at " 0 43 (:parent #165)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #165) #("guix-bioinformatics" 0 19 (:parent #169))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #165)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #165) #("PACKAGE" 0 7 (:parent #171))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #165) #("PATH" 0 4 (:parent #172))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #165))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #162) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #167))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #162) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #169))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #162) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #171))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #162) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #173)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #173) #("substitutes" 0 11 (:parent #177))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #173)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #173)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #173)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\"` switch.\n" 0 11 (:parent #173))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #162) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #174))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #162) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #176))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #160))) :mode nil :granularity nil :parent #151) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #160) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #163) #("Check out the source with git:\n" 0 31 (:parent #166))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #163) #("Run GN2 with above Guix profile\n" 0 32 (:parent #168))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #163) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #170))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #163) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #171))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #163) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #172))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #163) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #173))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #163) #("And browse on your local machine to " 0 36 (:parent #174)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #174)) #("\n" 0 1 (:parent #174))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #161))) :mode nil :granularity nil :parent #151) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #161) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #164) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #167)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #167) #("README" 0 6 (:parent #171))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #167))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #162))) :mode nil :granularity nil :parent #151) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #162) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #165) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #168))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #163))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #166))) :mode section :granularity nil :parent #163) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #166) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #169) #("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 #172))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #169) #("As root configure the Guix profile\n" 0 35 (:parent #173))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #169)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #169) #("and run for example\n" 0 20 (:parent #175))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #169)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #169) #("If you want to run as root you may have to set\n" 0 47 (:parent #177))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #169)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #169) #("You also need to set\n" 0 21 (:parent #179))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #169)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #169) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #181))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #169) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #182))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #169)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #169) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #184))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #169)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #169) #("When you get errors like:\n" 0 26 (:parent #186))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #169)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #169) #("you may need to set\n" 0 20 (:parent #188))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #169)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #167))) :mode nil :granularity nil :parent #163) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #167) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #170) #("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 #173)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #173) #("webqtl" 0 6 (:parent #177))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #173) #("s" 0 1 (:parent #178))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #173)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #173) #("webqtl" 0 6 (:parent #180))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #173) #("plant" 0 5 (:parent #181))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #173))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #170) #("Download one database from\n" 0 27 (:parent #174))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #170) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #175)) #("\n" 0 1 (:parent #175))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #170) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #176))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #170) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #178))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #170)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #170) #("and\n" 0 4 (:parent #181))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #170) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #183))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #170) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #185))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #170) #("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 #186))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #170) #("Note for the plant database you can rename it to db" 0 51 (:parent #187)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #187) #("webqtl" 0 6 (:parent #191))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #187) #("s" 0 1 (:parent #192))) #(", or\nchange the settings in etc/default" 0 39 (:parent #187)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #187) #("settings.py" 0 11 (:parent #194))) #("to match your path.\n" 0 20 (:parent #187)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #164))) :mode nil :granularity nil :parent #151) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #164) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #167) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #170)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #("\n" 0 1 (:parent #170))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #167)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #165))) :mode nil :granularity nil :parent #151) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #165) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #168) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #171))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #168) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n" 0 1 (:parent #172))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #166))) :mode nil :granularity nil :parent #151) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #166) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #169) #("See " 0 4 (:parent #172)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #(".\n" 0 2 (:parent #172))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #167))) :mode nil :granularity nil :parent #151) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #167) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #170) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #173)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #173))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #168))) :mode nil :granularity nil :parent #151) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #171))) :mode section :granularity nil :parent #168) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #171) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #174) #("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 #177)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #177) #("PATH" 0 4 (:parent #181))) #("and R" 0 5 (:parent #177)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #177) #("LIBS" 0 4 (:parent #183))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #177) #("SITE" 0 4 (:parent #184))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #177))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #174)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #174) #("On one system:\n" 0 15 (:parent #179))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #174)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #174) #("and perhaps a few more.\n" 0 24 (:parent #181))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #172)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #172) #("data" 0 4 (:parent #214))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #172)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #172) #("files" 0 5 (:parent #216))) #("/genotype'" 0 10 (:parent #172))) :mode nil :granularity nil :parent #168) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #172) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #175) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #178)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #178) #("data" 0 4 (:parent #182))) #(". 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 #178)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #178) #("settings.py" 0 11 (:parent #184))) #("(see above in\nthis document).\n" 0 30 (:parent #178))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #175) #("You can use the GENENETWORK" 0 27 (:parent #179)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #179) #("FILES" 0 5 (:parent #183))) #("switch to set the datadir, for example\n" 0 39 (:parent #179))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #175)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #173))) :mode nil :granularity nil :parent #168) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #173) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #176) #("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 #179))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #174))) :mode nil :granularity nil :parent #168) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #174) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #177) #("This error\n" 0 11 (:parent #180))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #177)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #177) #("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 #182))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #177) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #183)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #183) #("LIBS" 0 4 (:parent #187))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #183) #("SITE" 0 4 (:parent #188))) #(". 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 #183))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #175))) :mode nil :granularity nil :parent #168) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #175) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #178) #("The following error\n" 0 20 (:parent #181))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #178)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #178) #("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 #183))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #178)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #178) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #185))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #178)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #178) #("if that works run genenetwork after setting SQL" 0 47 (:parent #187)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #187) #("URI" 0 3 (:parent #191))) #("to something like\n" 0 18 (:parent #187))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #178))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #169))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #172))) :mode section :granularity nil :parent #169) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #172) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #175) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #178))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #175) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #182) #("Base install\n" 0 13 (:parent #185))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #182) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #189) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #192)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #186) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #190) #("Get Guix build going\n" 0 21 (:parent #193))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #166) #("Redis\n" 0 6 (:parent #169)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #167) #("Mariadb\n" 0 8 (:parent #170))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #153) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #156) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #159)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #159))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #154))) :mode nil :granularity nil :parent #146) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #154) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #157) #("We run a GNU Guix channel with packages at " 0 43 (:parent #160)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #160) #("guix-bioinformatics" 0 19 (:parent #164))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #160)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #166))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #160) #("PATH" 0 4 (:parent #167))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #160))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #157) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #162))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #157) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #164))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #157) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #166))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #157)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #157) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #168)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #168) #("substitutes" 0 11 (:parent #172))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #168)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #168)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #168)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\"` switch.\n" 0 11 (:parent #168))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #157) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #169))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #157)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #157) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #171))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #155) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #158) #("Check out the source with git:\n" 0 31 (:parent #161))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #158)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #158) #("Run GN2 with above Guix profile\n" 0 32 (:parent #163))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #158)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #158) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #165))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #158) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #166))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #158) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #167))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #158) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #168))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #158) #("And browse on your local machine to " 0 36 (:parent #169)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #("\n" 0 1 (:parent #169))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #156))) :mode nil :granularity nil :parent #146) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #156) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #159) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #162)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #162) #("README" 0 6 (:parent #166))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #162))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #157) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #160) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #163))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #158))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #161))) :mode section :granularity nil :parent #158) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #161) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #164) #("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 #167))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #164) #("As root configure the Guix profile\n" 0 35 (:parent #168))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #164) #("and run for example\n" 0 20 (:parent #170))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #164) #("If you want to run as root you may have to set\n" 0 47 (:parent #172))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #164) #("You also need to set\n" 0 21 (:parent #174))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #164) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #176))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #164) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #177))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #164) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #179))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #164) #("When you get errors like:\n" 0 26 (:parent #181))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #164) #("you may need to set\n" 0 20 (:parent #183))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #164)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #162))) :mode nil :granularity nil :parent #158) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #162) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #165) #("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 #168)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #168) #("s" 0 1 (:parent #173))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #168)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #175))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #168) #("plant" 0 5 (:parent #176))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #168))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #165) #("Download one database from\n" 0 27 (:parent #169))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #165) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #("\n" 0 1 (:parent #170))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #165) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #171))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #165) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #173))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #165)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #165) #("and\n" 0 4 (:parent #176))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #165) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #178))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #165) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #180))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #165) #("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 #181))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #165) #("Note for the plant database you can rename it to db" 0 51 (:parent #182)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #182) #("webqtl" 0 6 (:parent #186))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #182) #("s" 0 1 (:parent #187))) #(", or\nchange the settings in etc/default" 0 39 (:parent #182)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #182) #("settings.py" 0 11 (:parent #189))) #("to match your path.\n" 0 20 (:parent #182)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #159) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #162) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #165)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #("\n" 0 1 (:parent #165))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #162)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #160))) :mode nil :granularity nil :parent #146) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #160) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #163) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #166))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #163) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #161))) :mode nil :granularity nil :parent #146) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #161) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #164) #("See " 0 4 (:parent #167)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(".\n" 0 2 (:parent #167))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #162))) :mode nil :granularity nil :parent #146) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #162) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #165) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #168)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #168))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #163))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #166))) :mode section :granularity nil :parent #163) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #166) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #169) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #172)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #172) #("PATH" 0 4 (:parent #176))) #("and R" 0 5 (:parent #172)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #172) #("LIBS" 0 4 (:parent #178))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #172) #("SITE" 0 4 (:parent #179))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #172))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #169)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #169) #("On one system:\n" 0 15 (:parent #174))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #169)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #169) #("and perhaps a few more.\n" 0 24 (:parent #176))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #167)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #167) #("data" 0 4 (:parent #209))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #167)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #167) #("files" 0 5 (:parent #211))) #("/genotype'" 0 10 (:parent #167))) :mode nil :granularity nil :parent #163) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #167) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #170) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #173)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #173) #("data" 0 4 (:parent #177))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #173)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #173) #("settings.py" 0 11 (:parent #179))) #("(see above in\nthis document).\n" 0 30 (:parent #173))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #170) #("You can use the GENENETWORK" 0 27 (:parent #174)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #174) #("FILES" 0 5 (:parent #178))) #("switch to set the datadir, for example\n" 0 39 (:parent #174))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #170)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #168))) :mode nil :granularity nil :parent #163) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #168) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #171) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #174))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #169))) :mode nil :granularity nil :parent #163) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #169) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #172) #("This error\n" 0 11 (:parent #175))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #172)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #172) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #177))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #172) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #178)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #178) #("LIBS" 0 4 (:parent #182))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #178) #("SITE" 0 4 (:parent #183))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #178))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #170))) :mode nil :granularity nil :parent #163) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #170) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #173) #("The following error\n" 0 20 (:parent #176))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #173)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #173) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #178))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #173)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #173) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #180))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #173)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #173) #("if that works run genenetwork after setting SQL" 0 47 (:parent #182)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #182) #("URI" 0 3 (:parent #186))) #("to something like\n" 0 18 (:parent #182))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #173))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #164))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #167))) :mode section :granularity nil :parent #164) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #167) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #170) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #173))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #193) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #196)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #186) #("Create a gn2 user and home with space\n" 0 38 (:parent #189)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#187) #("Install redis\n" 0 14 (:parent #190))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #187) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #194) #("add to systemd\n" 0 15 (:parent #197)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #191) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #195) #("update redis.cnf\n" 0 17 (:parent #198)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #191) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #196) #("update database\n" 0 16 (:parent #199)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #343) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #347) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #354) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #357)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #362) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #366) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #369) #("Base install\n" 0 13 (:parent #372))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #369) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #376) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #379)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #377) #("Get Guix build going\n" 0 21 (:parent #380))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #377) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #384) #("Build the correct version of Guix\n" 0 34 (:parent #387)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #386) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #389)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #378) #("Create a gn2 user and home with space\n" 0 38 (:parent #381)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #379) #("Install redis\n" 0 14 (:parent #382))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #379) (item (:bullet "- " :begin 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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 #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #163))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #158) #("GNU Guix" 0 8 (:parent #164))) #(".\n" 0 2 (:parent #158))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #154) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #159)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #159) #("GN2 Dependency Graph" 0 20 (:parent #163))) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #152) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #155) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #158))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #155) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #162) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #165)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #163) #("A path to the (static) genotype files\n" 0 38 (:parent #166)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #164) #("Gn-proxy for authentication\n" 0 28 (:parent #167)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #165) #("The genenetwork3 service\n" 0 25 (:parent #168)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #166) #("Redis\n" 0 6 (:parent #169)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #167) #("Mariadb\n" 0 8 (:parent #170))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #153) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #156) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #159)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #159))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #154))) :mode nil :granularity nil :parent #146) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #154) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #157) #("We run a GNU Guix channel with packages at " 0 43 (:parent #160)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #160) #("guix-bioinformatics" 0 19 (:parent #164))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #160)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #160) #("PACKAGE" 0 7 (:parent #166))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #160) #("PATH" 0 4 (:parent #167))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #160))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #157) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #162))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #157) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #164))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #157)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #157) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #166))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #157)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #157) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #168)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #168) #("substitutes" 0 11 (:parent #172))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #168)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #168)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #168)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\"` switch.\n" 0 11 (:parent #168))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #157) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #169))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #157)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #157) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #171))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #155) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #158) #("Check out the source with git:\n" 0 31 (:parent #161))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #158)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #158) #("Run GN2 with above Guix profile\n" 0 32 (:parent #163))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #158)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #158) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #165))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #158) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #166))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #158) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #167))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #158) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #168))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #158) #("And browse on your local machine to " 0 36 (:parent #169)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #("\n" 0 1 (:parent #169))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #156))) :mode nil :granularity nil :parent #146) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #156) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #159) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #162)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #162) #("README" 0 6 (:parent #166))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #162))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #157) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #160) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #163))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #158))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #161))) :mode section :granularity nil :parent #158) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #161) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #164) #("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 #167))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #164) #("As root configure the Guix profile\n" 0 35 (:parent #168))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #164) #("and run for example\n" 0 20 (:parent #170))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #164)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #164) #("If you want to run as root you may have to set\n" 0 47 (:parent #172))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #164) #("You also need to set\n" 0 21 (:parent #174))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #164) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #176))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #164) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #177))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #164) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #179))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #164) #("When you get errors like:\n" 0 26 (:parent #181))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #164)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #164) #("you may need to set\n" 0 20 (:parent #183))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #164)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #162))) :mode nil :granularity nil :parent #158) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #162) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #165) #("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 #168)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #168) #("s" 0 1 (:parent #173))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #168)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #175))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #168) #("plant" 0 5 (:parent #176))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #168))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #165) #("Download one database from\n" 0 27 (:parent #169))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #165) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #("\n" 0 1 (:parent #170))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #165) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #171))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #165) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #173))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #165)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #165) #("and\n" 0 4 (:parent #176))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #165) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #178))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #165)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #165) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #180))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #165) #("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 #181))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #165) #("Note for the plant database you can rename it to db" 0 51 (:parent #182)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #182) #("webqtl" 0 6 (:parent #186))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #182) #("s" 0 1 (:parent #187))) #(", or\nchange the settings in etc/default" 0 39 (:parent #182)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #182) #("settings.py" 0 11 (:parent #189))) #("to match your path.\n" 0 20 (:parent #182)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #159) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #162) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #165)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #("\n" 0 1 (:parent #165))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #162)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #160))) :mode nil :granularity nil :parent #146) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #160) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #163) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #166))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #163) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #161))) :mode nil :granularity nil :parent #146) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #161) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #164) #("See " 0 4 (:parent #167)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(".\n" 0 2 (:parent #167))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #162))) :mode nil :granularity nil :parent #146) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #162) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #165) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #168)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #168))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #163))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #166))) :mode section :granularity nil :parent #163) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #166) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #169) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #172)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #172) #("PATH" 0 4 (:parent #176))) #("and R" 0 5 (:parent #172)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #172) #("LIBS" 0 4 (:parent #178))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #172) #("SITE" 0 4 (:parent #179))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #172))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #169)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #169) #("On one system:\n" 0 15 (:parent #174))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #169)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #169) #("and perhaps a few more.\n" 0 24 (:parent #176))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #167)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #167) #("data" 0 4 (:parent #209))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #167)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #167) #("files" 0 5 (:parent #211))) #("/genotype'" 0 10 (:parent #167))) :mode nil :granularity nil :parent #163) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #167) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #170) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #173)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #173) #("data" 0 4 (:parent #177))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #173)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #173) #("settings.py" 0 11 (:parent #179))) #("(see above in\nthis document).\n" 0 30 (:parent #173))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #170) #("You can use the GENENETWORK" 0 27 (:parent #174)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #174) #("FILES" 0 5 (:parent #178))) #("switch to set the datadir, for example\n" 0 39 (:parent #174))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #170)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #168))) :mode nil :granularity nil :parent #163) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #168) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #171) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #174))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #169))) :mode nil :granularity nil :parent #163) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #169) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #172) #("This error\n" 0 11 (:parent #175))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #172)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #172) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #177))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #172) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #178)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #178) #("LIBS" 0 4 (:parent #182))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #178) #("SITE" 0 4 (:parent #183))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #178))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #170))) :mode nil :granularity nil :parent #163) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #170) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #173) #("The following error\n" 0 20 (:parent #176))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #173)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #173) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #178))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #173)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #173) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #180))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #173)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #173) #("if that works run genenetwork after setting SQL" 0 47 (:parent #182)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #182) #("URI" 0 3 (:parent #186))) #("to something like\n" 0 18 (:parent #182))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #173))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #164))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #167))) :mode section :granularity nil :parent #164) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #167) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #170) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #173))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #170) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #174) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #177) #("Base install\n" 0 13 (:parent #180))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #177) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #184) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #187)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #185) #("Get Guix build going\n" 0 21 (:parent #188))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #185) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #192) #("Build the correct version of Guix\n" 0 34 (:parent #195)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #193) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #196)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #189) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #194) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #197)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #186) #("Create a gn2 user and home with space\n" 0 38 (:parent #189)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #187) #("Install redis\n" 0 14 (:parent #190))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #187) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #191) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #194) #("add to systemd\n" 0 15 (:parent #197)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #191) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #195) #("update redis.cnf\n" 0 17 (:parent #198)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #191) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #196) #("update database\n" 0 16 (:parent #199)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(section (:begin 121 :end 1439 :contents-begin 121 :contents-end 1438 :robust-begin 121 :robust-end 1436 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1439 :pre-blank 0 :contents-begin 121 :contents-end 1438 :robust-begin 123 :robust-end 1436 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #101))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #147) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #150))) #101 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #152) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #155) #("Large system deployments can get very " 0 38 (:parent #158)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket 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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 #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #158) #("Guix-notes" 0 10 (:parent #164))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #158))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #155) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #159) #("Guix bioinformatics" 0 19 (:parent #163))) #("and " 0 4 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #159) #("GNU Guix" 0 8 (:parent #165))) #(".\n" 0 2 (:parent #159))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #155) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #160)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #160) #("GN2 Dependency Graph" 0 20 (:parent #164))) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #153) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #156) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #159))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #164) #("A path to the (static) genotype files\n" 0 38 (:parent #167)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #165) #("Gn-proxy for authentication\n" 0 28 (:parent #168)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #166) #("The genenetwork3 service\n" 0 25 (:parent #169)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #167) #("Redis\n" 0 6 (:parent #170)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #168) #("Mariadb\n" 0 8 (:parent #171))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #154) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #157) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #160)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #160)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #160))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #157)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #155))) :mode nil :granularity nil :parent #147) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #155) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #158) #("We run a GNU Guix channel with packages at " 0 43 (:parent #161)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #161) #("guix-bioinformatics" 0 19 (:parent #165))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #161)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #161) #("PACKAGE" 0 7 (:parent #167))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #161) #("PATH" 0 4 (:parent #168))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #161))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #158)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #158) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #163))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #158)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #158) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #165))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #158)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #158) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #167))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #158)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #158) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #169)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #169) #("substitutes" 0 11 (:parent #173))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #169)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #169)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #169)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #("\"` switch.\n" 0 11 (:parent #169))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #158) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #170))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #158)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #158) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #172))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #156))) :mode nil :granularity nil :parent #147) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #156) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #159) #("Check out the source with git:\n" 0 31 (:parent #162))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #159)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #159) #("Run GN2 with above Guix profile\n" 0 32 (:parent #164))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #159)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #159) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #166))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #159) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #167))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #159) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #168))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #159) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #169))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #159) #("And browse on your local machine to " 0 36 (:parent #170)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #("\n" 0 1 (:parent #170))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #157))) :mode nil :granularity nil :parent #147) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #157) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #160) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #163)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #163) #("README" 0 6 (:parent #167))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #163))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #158))) :mode nil :granularity nil :parent #147) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #158) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #161) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #164))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #159))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #162))) :mode section :granularity nil :parent #159) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #162) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #165) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #168))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #165) #("As root configure the Guix profile\n" 0 35 (:parent #169))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #165)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #165) #("and run for example\n" 0 20 (:parent #171))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #165)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #165) #("If you want to run as root you may have to set\n" 0 47 (:parent #173))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #165)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #165) #("You also need to set\n" 0 21 (:parent #175))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #165)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #165) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #177))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #165) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #178))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #165)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #165) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #180))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #165)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #165) #("When you get errors like:\n" 0 26 (:parent #182))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #165)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #165) #("you may need to set\n" 0 20 (:parent #184))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #163))) :mode nil :granularity nil :parent #159) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #163) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #166) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #169)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #169)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #176))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #169) #("plant" 0 5 (:parent #177))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #169))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #166) #("Download one database from\n" 0 27 (:parent #170))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #166) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #171)) #("\n" 0 1 (:parent #171))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #166) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #172))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #166)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #166) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #174))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #166)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #166)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #166) #("and\n" 0 4 (:parent #177))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #166)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #166) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #179))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #166)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #166) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #181))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #166) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #182))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #166) #("Note for the plant database you can rename it to db" 0 51 (:parent #183)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #183) #("webqtl" 0 6 (:parent #187))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #183) #("s" 0 1 (:parent #188))) #(", or\nchange the settings in etc/default" 0 39 (:parent #183)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #183) #("settings.py" 0 11 (:parent #190))) #("to match your path.\n" 0 20 (:parent #183)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #160))) :mode nil :granularity nil :parent #147) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #160) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #163) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #166)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #("\n" 0 1 (:parent #166))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #163)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #161))) :mode nil :granularity nil :parent #147) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #161) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #164) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #167))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #164) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\n" 0 1 (:parent #168))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #162))) :mode nil :granularity nil :parent #147) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #162) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #165) #("See " 0 4 (:parent #168)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #(".\n" 0 2 (:parent #168))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #163))) :mode nil :granularity nil :parent #147) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #163) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #166) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #169)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #169))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #164))) :mode nil :granularity nil :parent #147) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #167))) :mode section :granularity nil :parent #164) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #167) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #170) #("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 #173)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #173) #("PATH" 0 4 (:parent #177))) #("and R" 0 5 (:parent #173)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #173) #("LIBS" 0 4 (:parent #179))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #173) #("SITE" 0 4 (:parent #180))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #173))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #170)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #170) #("On one system:\n" 0 15 (:parent #175))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #170)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #170) #("and perhaps a few more.\n" 0 24 (:parent #177))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #168)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #168) #("data" 0 4 (:parent #210))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #168)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #168) #("files" 0 5 (:parent #212))) #("/genotype'" 0 10 (:parent #168))) :mode nil :granularity nil :parent #164) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #168) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #171) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #174)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #174) #("data" 0 4 (:parent #178))) #(". 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 #174)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #174) #("settings.py" 0 11 (:parent #180))) #("(see above in\nthis document).\n" 0 30 (:parent #174))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #171) #("You can use the GENENETWORK" 0 27 (:parent #175)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #175) #("FILES" 0 5 (:parent #179))) #("switch to set the datadir, for example\n" 0 39 (:parent #175))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #171)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #169))) :mode nil :granularity nil :parent #164) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #169) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #172) #("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 #175))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #170))) :mode nil :granularity nil :parent #164) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #170) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #173) #("This error\n" 0 11 (:parent #176))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #173)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #173) #("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 #178))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #173) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #179)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #179) #("LIBS" 0 4 (:parent #183))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #179) #("SITE" 0 4 (:parent #184))) #(". 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 #179))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #171))) :mode nil :granularity nil :parent #164) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #171) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #174) #("The following error\n" 0 20 (:parent #177))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #174)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #174) #("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 #179))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #174)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #174) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #181))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #174)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #174) #("if that works run genenetwork after setting SQL" 0 47 (:parent #183)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #183) #("URI" 0 3 (:parent #187))) #("to something like\n" 0 18 (:parent #183))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #174))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #165))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #168))) :mode section :granularity nil :parent #165) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #168) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #171) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #174))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #171) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #175) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #178) #("Base install\n" 0 13 (:parent #181))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #178) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #182) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #185) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #188)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #182) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #186) #("Get Guix build going\n" 0 21 (:parent #189))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #146) #("Redis\n" 0 6 (:parent #149)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #147) #("Mariadb\n" 0 8 (:parent #150))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #133) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #136) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #139)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #139)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #139))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #136)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #134))) :mode nil :granularity nil :parent #126) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #134) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #137) #("We run a GNU Guix channel with packages at " 0 43 (:parent #140)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #140) #("guix-bioinformatics" 0 19 (:parent #144))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #140)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #140) #("PACKAGE" 0 7 (:parent #146))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #140) #("PATH" 0 4 (:parent #147))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #140))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #137) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #142))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #137) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #144))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #137) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #146))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #137)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #137) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #148)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #148) #("substitutes" 0 11 (:parent #152))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #148)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\"` switch.\n" 0 11 (:parent #148))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #137) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #149))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #137)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #137) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #151))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #135) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #138) #("Check out the source with git:\n" 0 31 (:parent #141))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #138)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #138) #("Run GN2 with above Guix profile\n" 0 32 (:parent #143))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #138)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #138) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #145))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #138) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #146))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #138) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #147))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #138) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #148))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #138) #("And browse on your local machine to " 0 36 (:parent #149)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #136))) :mode nil :granularity nil :parent #126) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #136) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #139) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #142)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #142) #("README" 0 6 (:parent #146))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #142))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #137) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #140) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #143))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #138))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #141) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #144) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #147))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #144) #("As root configure the Guix profile\n" 0 35 (:parent #148))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #144) #("and run for example\n" 0 20 (:parent #150))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #144) #("If you want to run as root you may have to set\n" 0 47 (:parent #152))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #144) #("You also need to set\n" 0 21 (:parent #154))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #144) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #156))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #144) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #157))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #144) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #159))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #144) #("When you get errors like:\n" 0 26 (:parent #161))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #144) #("you may need to set\n" 0 20 (:parent #163))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #142) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #145) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #148)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #152))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #148) #("s" 0 1 (:parent #153))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #148)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #148) #("plant" 0 5 (:parent #156))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #148))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #145) #("Download one database from\n" 0 27 (:parent #149))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #145) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #145) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #151))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #145) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #153))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #145)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #145) #("and\n" 0 4 (:parent #156))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #145) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #158))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #145) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #160))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #145) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #161))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #145) #("Note for the plant database you can rename it to db" 0 51 (:parent #162)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #162) #("s" 0 1 (:parent #167))) #(", or\nchange the settings in etc/default" 0 39 (:parent #162)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #169))) #("to match your path.\n" 0 20 (:parent #162)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #139) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #142) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #145)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #140))) :mode nil :granularity nil :parent #126) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #140) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #143) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #146))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #143) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #141))) :mode nil :granularity nil :parent #126) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #141) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #144) #("See " 0 4 (:parent #147)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #142))) :mode nil :granularity nil :parent #126) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #142) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #145) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #148)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #148))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #143))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #146) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #149) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #152)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #152) #("PATH" 0 4 (:parent #156))) #("and R" 0 5 (:parent #152)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #152) #("LIBS" 0 4 (:parent #158))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #152) #("SITE" 0 4 (:parent #159))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #152))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #149)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #149) #("On one system:\n" 0 15 (:parent #154))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #149)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #149) #("and perhaps a few more.\n" 0 24 (:parent #156))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #147)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #147) #("data" 0 4 (:parent #189))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #147)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #147) #("files" 0 5 (:parent #191))) #("/genotype'" 0 10 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #147) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #150) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #153)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #153) #("data" 0 4 (:parent #157))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #153)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #153) #("settings.py" 0 11 (:parent #159))) #("(see above in\nthis document).\n" 0 30 (:parent #153))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #150) #("You can use the GENENETWORK" 0 27 (:parent #154)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #154) #("FILES" 0 5 (:parent #158))) #("switch to set the datadir, for example\n" 0 39 (:parent #154))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #148))) :mode nil :granularity nil :parent #143) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #148) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #151) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #154))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #149))) :mode nil :granularity nil :parent #143) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #149) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #152) #("This error\n" 0 11 (:parent #155))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #152)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #152) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #157))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #152) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #158)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #158) #("SITE" 0 4 (:parent #163))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #158))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #150))) :mode nil :granularity nil :parent #143) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #150) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #153) #("The following error\n" 0 20 (:parent #156))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #153)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #153) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #158))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #153)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #153) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #160))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #153)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #153) #("if that works run genenetwork after setting SQL" 0 47 (:parent #162)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #162) #("URI" 0 3 (:parent #166))) #("to something like\n" 0 18 (:parent #162))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #153))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #144))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #147) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #150) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #153))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #173) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #176)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #176)) #("\n" 0 1 (:parent #176)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #166) #("Create a gn2 user and home with space\n" 0 38 (:parent #169)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#167) #("Install redis\n" 0 14 (:parent #170))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #167) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #174) #("add to systemd\n" 0 15 (:parent #177)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #175) #("update redis.cnf\n" 0 17 (:parent #178)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #176) #("update database\n" 0 16 (:parent #179)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #343) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #347) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #354) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #357)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #362) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #366) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #369) #("Base install\n" 0 13 (:parent #372))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #369) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #376) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #379)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #377) #("Get Guix build going\n" 0 21 (:parent #380))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #377) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #384) #("Build the correct version of Guix\n" 0 34 (:parent #387)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #131))) :mode nil :granularity nil :parent #126) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #131) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #134) #("Large system deployments can get very " 0 38 (:parent #137)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 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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 #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #143))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #138) #("GNU Guix" 0 8 (:parent #144))) #(".\n" 0 2 (:parent #138))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #134) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #139)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #139) #("GN2 Dependency Graph" 0 20 (:parent #143))) #(".\n" 0 2 (:parent #139))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #132))) :mode nil :granularity nil :parent #126) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #132) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #135) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #138))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #135) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #142) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #145)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #143) #("A path to the (static) genotype files\n" 0 38 (:parent #146)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #144) #("Gn-proxy for authentication\n" 0 28 (:parent #147)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #145) #("The genenetwork3 service\n" 0 25 (:parent #148)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #146) #("Redis\n" 0 6 (:parent #149)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #147) #("Mariadb\n" 0 8 (:parent #150))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #133) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #136) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #139)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #139)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #139))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #136)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #134))) :mode nil :granularity nil :parent #126) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #134) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #137) #("We run a GNU Guix channel with packages at " 0 43 (:parent #140)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #140) #("guix-bioinformatics" 0 19 (:parent #144))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #140)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #140) #("PACKAGE" 0 7 (:parent #146))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #140) #("PATH" 0 4 (:parent #147))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #140))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #137) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #142))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #137) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #144))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #137)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #137) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #146))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #137)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #137) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #148)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #148) #("substitutes" 0 11 (:parent #152))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #148)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\"` switch.\n" 0 11 (:parent #148))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #137) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #149))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #137)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #137) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #151))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #135) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #138) #("Check out the source with git:\n" 0 31 (:parent #141))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #138)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #138) #("Run GN2 with above Guix profile\n" 0 32 (:parent #143))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #138)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #138) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #145))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #138) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #146))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #138) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #147))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #138) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #148))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #138) #("And browse on your local machine to " 0 36 (:parent #149)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #136))) :mode nil :granularity nil :parent #126) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #136) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #139) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #142)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #142) #("README" 0 6 (:parent #146))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #142))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #137) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #140) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #143))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #138))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #141) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #144) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #147))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #144) #("As root configure the Guix profile\n" 0 35 (:parent #148))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #144) #("and run for example\n" 0 20 (:parent #150))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #144)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #144) #("If you want to run as root you may have to set\n" 0 47 (:parent #152))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #144) #("You also need to set\n" 0 21 (:parent #154))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #144) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #156))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #144) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #157))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #144) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #159))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #144) #("When you get errors like:\n" 0 26 (:parent #161))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #144)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #144) #("you may need to set\n" 0 20 (:parent #163))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #142) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #145) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #148)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #152))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #148) #("s" 0 1 (:parent #153))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #148)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #148) #("plant" 0 5 (:parent #156))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #148))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #145) #("Download one database from\n" 0 27 (:parent #149))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #145) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #145) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #151))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #145) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #153))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #145)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #145) #("and\n" 0 4 (:parent #156))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #145) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #158))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #145)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #145) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #160))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #145) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #161))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #145) #("Note for the plant database you can rename it to db" 0 51 (:parent #162)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #162) #("s" 0 1 (:parent #167))) #(", or\nchange the settings in etc/default" 0 39 (:parent #162)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #169))) #("to match your path.\n" 0 20 (:parent #162)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #139) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #142) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #145)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #140))) :mode nil :granularity nil :parent #126) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #140) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #143) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #146))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #143) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #141))) :mode nil :granularity nil :parent #126) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #141) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #144) #("See " 0 4 (:parent #147)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #142))) :mode nil :granularity nil :parent #126) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #142) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #145) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #148)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #148))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #143))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #146) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #149) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #152)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #152) #("PATH" 0 4 (:parent #156))) #("and R" 0 5 (:parent #152)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #152) #("LIBS" 0 4 (:parent #158))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #152) #("SITE" 0 4 (:parent #159))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #152))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #149)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #149) #("On one system:\n" 0 15 (:parent #154))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #149)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #149) #("and perhaps a few more.\n" 0 24 (:parent #156))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #147)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #147) #("data" 0 4 (:parent #189))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #147)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #147) #("files" 0 5 (:parent #191))) #("/genotype'" 0 10 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #147) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #150) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #153)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #153) #("data" 0 4 (:parent #157))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #153)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #153) #("settings.py" 0 11 (:parent #159))) #("(see above in\nthis document).\n" 0 30 (:parent #153))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #150) #("You can use the GENENETWORK" 0 27 (:parent #154)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #154) #("FILES" 0 5 (:parent #158))) #("switch to set the datadir, for example\n" 0 39 (:parent #154))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #148))) :mode nil :granularity nil :parent #143) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #148) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #151) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #154))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #149))) :mode nil :granularity nil :parent #143) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #149) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #152) #("This error\n" 0 11 (:parent #155))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #152)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #152) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #157))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #152) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #158)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #158) #("SITE" 0 4 (:parent #163))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #158))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #150))) :mode nil :granularity nil :parent #143) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #150) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #153) #("The following error\n" 0 20 (:parent #156))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #153)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #153) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #158))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #153)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #153) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #160))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #153)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #153) #("if that works run genenetwork after setting SQL" 0 47 (:parent #162)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #162) #("URI" 0 3 (:parent #166))) #("to something like\n" 0 18 (:parent #162))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #153))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #144))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #147) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #150) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #153))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #150) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #154) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #157) #("Base install\n" 0 13 (:parent #160))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #157) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #164) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #167)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #165) #("Get Guix build going\n" 0 21 (:parent #168))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #165) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #172) #("Build the correct version of Guix\n" 0 34 (:parent #175)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #173) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #176)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #176)) #("\n" 0 1 (:parent #176)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #174) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #177)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #166) #("Create a gn2 user and home with space\n" 0 38 (:parent #169)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #167) #("Install redis\n" 0 14 (:parent #170))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #167) (item (:bullet "- " :begin 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(section (:begin 121 :end 1439 :contents-begin 121 :contents-end 1438 :robust-begin 121 :robust-end 1436 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1439 :pre-blank 0 :contents-begin 121 :contents-end 1438 :robust-begin 123 :robust-end 1436 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #81))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #127) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #130))) #81 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #132))) :mode nil :granularity nil :parent #127) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #132) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #135) #("Large system deployments can get very " 0 38 (:parent #138)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket 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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 #138)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #138) #("Guix-notes" 0 10 (:parent #144))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #138))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #135) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #139) #("Guix bioinformatics" 0 19 (:parent #143))) #("and " 0 4 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #139) #("GNU Guix" 0 8 (:parent #145))) #(".\n" 0 2 (:parent #139))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #135) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #140)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #140) #("GN2 Dependency Graph" 0 20 (:parent #144))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #133))) :mode nil :granularity nil :parent #127) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #133) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #136) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #139))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #140) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #147) #("Redis\n" 0 6 (:parent #150)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. 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Follow the instructions on\n" 0 117 (:parent #140)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #140)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #140))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #137)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #135))) :mode nil :granularity nil :parent #127) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #135) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #138) #("We run a GNU Guix channel with packages at " 0 43 (:parent #141)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #141) #("guix-bioinformatics" 0 19 (:parent #145))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #141)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #141) #("PACKAGE" 0 7 (:parent #147))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #141) #("PATH" 0 4 (:parent #148))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #141))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #138)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #138) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #143))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #138)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #138) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #145))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #138)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #138) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #147))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #138)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #138) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #149)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #149) #("substitutes" 0 11 (:parent #153))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #149)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #149)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #149)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\"` switch.\n" 0 11 (:parent #149))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #138) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #150))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #138)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #138) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #152))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #136))) :mode nil :granularity nil :parent #127) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #136) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #139) #("Check out the source with git:\n" 0 31 (:parent #142))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #139)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #139) #("Run GN2 with above Guix profile\n" 0 32 (:parent #144))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #139)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #139) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #146))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #139) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #147))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #139) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #148))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #139) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #149))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #139) #("And browse on your local machine to " 0 36 (:parent #150)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #137))) :mode nil :granularity nil :parent #127) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #137) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #140) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #143) #("README" 0 6 (:parent #147))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #143))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #138))) :mode nil :granularity nil :parent #127) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #138) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #141) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #144))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #139))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #142))) :mode section :granularity nil :parent #139) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #142) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #145) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #148))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #145) #("As root configure the Guix profile\n" 0 35 (:parent #149))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #145)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #145) #("and run for example\n" 0 20 (:parent #151))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #145)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #145) #("If you want to run as root you may have to set\n" 0 47 (:parent #153))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #145)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #145) #("You also need to set\n" 0 21 (:parent #155))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #145)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #145) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #157))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #145) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #158))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #145)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #145) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #160))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #145)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #145) #("When you get errors like:\n" 0 26 (:parent #162))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #145)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #145) #("you may need to set\n" 0 20 (:parent #164))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #143))) :mode nil :granularity nil :parent #139) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #143) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #146) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #149)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #149) #("s" 0 1 (:parent #154))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #149)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #149) #("plant" 0 5 (:parent #157))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #149))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #146) #("Download one database from\n" 0 27 (:parent #150))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #146) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #146) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #152))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #146)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #146) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #154))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #146)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #146)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #146) #("and\n" 0 4 (:parent #157))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #146)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #146) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #159))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #146)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #146) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #161))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #146) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #162))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #146) #("Note for the plant database you can rename it to db" 0 51 (:parent #163)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #163) #("webqtl" 0 6 (:parent #167))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #163) #("s" 0 1 (:parent #168))) #(", or\nchange the settings in etc/default" 0 39 (:parent #163)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #163) #("settings.py" 0 11 (:parent #170))) #("to match your path.\n" 0 20 (:parent #163)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #140))) :mode nil :granularity nil :parent #127) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #140) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #143) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #146)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #143)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #141))) :mode nil :granularity nil :parent #127) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #141) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #144) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #147))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #144) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #142))) :mode nil :granularity nil :parent #127) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #142) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #145) #("See " 0 4 (:parent #148)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #143))) :mode nil :granularity nil :parent #127) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #143) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #146) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #149)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #149))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #144))) :mode nil :granularity nil :parent #127) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #147) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #150) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #153)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #153) #("PATH" 0 4 (:parent #157))) #("and R" 0 5 (:parent #153)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #153) #("LIBS" 0 4 (:parent #159))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #153) #("SITE" 0 4 (:parent #160))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #153))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #150)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #150) #("On one system:\n" 0 15 (:parent #155))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #150)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #150) #("and perhaps a few more.\n" 0 24 (:parent #157))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #148)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #148) #("data" 0 4 (:parent #190))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #148)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #148) #("files" 0 5 (:parent #192))) #("/genotype'" 0 10 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #148) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #151) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #154)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #154) #("data" 0 4 (:parent #158))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #154)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #154) #("settings.py" 0 11 (:parent #160))) #("(see above in\nthis document).\n" 0 30 (:parent #154))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #151) #("You can use the GENENETWORK" 0 27 (:parent #155)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #155) #("FILES" 0 5 (:parent #159))) #("switch to set the datadir, for example\n" 0 39 (:parent #155))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #149))) :mode nil :granularity nil :parent #144) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #149) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #152) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #155))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #150))) :mode nil :granularity nil :parent #144) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #150) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #153) #("This error\n" 0 11 (:parent #156))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #153)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #153) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #158))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #153) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #159)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #159) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #159) #("SITE" 0 4 (:parent #164))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #159))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #151))) :mode nil :granularity nil :parent #144) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #151) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #154) #("The following error\n" 0 20 (:parent #157))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #154)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #154) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #159))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #154)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #154) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #161))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #154)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #154) #("if that works run genenetwork after setting SQL" 0 47 (:parent #163)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #163) #("URI" 0 3 (:parent #167))) #("to something like\n" 0 18 (:parent #163))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #154))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #145))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #148) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #151) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #154))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #175) #("add to systemd\n" 0 15 (:parent #178)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #139)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #139) #("Guix-notes" 0 10 (:parent #145))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #139))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #136) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #140) #("Guix bioinformatics" 0 19 (:parent #144))) #("and " 0 4 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #140) #("GNU Guix" 0 8 (:parent #146))) #(".\n" 0 2 (:parent #140))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #136) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #141)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #141) #("GN2 Dependency Graph" 0 20 (:parent #145))) #(".\n" 0 2 (:parent #141))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #134))) :mode nil :granularity nil :parent #128) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #134) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #137) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #140))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #141) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #145) #("A path to the (static) genotype files\n" 0 38 (:parent #148)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #141) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #148) #("Redis\n" 0 6 (:parent #151)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. 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Follow the instructions on\n" 0 117 (:parent #141)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #141)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #141))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #138)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #136))) :mode nil :granularity nil :parent #128) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #136) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #139) #("We run a GNU Guix channel with packages at " 0 43 (:parent #142)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #142) #("guix-bioinformatics" 0 19 (:parent #146))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #142)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #142) #("PACKAGE" 0 7 (:parent #148))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #142) #("PATH" 0 4 (:parent #149))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #142))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #139)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #139) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #144))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #139)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #139) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #146))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #139)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #139) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #148))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #139)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #139) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #150)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #150) #("substitutes" 0 11 (:parent #154))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #150)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #150)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #150)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\"` switch.\n" 0 11 (:parent #150))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #139) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #151))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #139)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #139) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #153))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #137))) :mode nil :granularity nil :parent #128) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #137) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #140) #("Check out the source with git:\n" 0 31 (:parent #143))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #140)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #140) #("Run GN2 with above Guix profile\n" 0 32 (:parent #145))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #140)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #140) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #147))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #140) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #148))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #140) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #149))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #140) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #150))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #140) #("And browse on your local machine to " 0 36 (:parent #151)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #138))) :mode nil :granularity nil :parent #128) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #138) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #141) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #144)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #144) #("README" 0 6 (:parent #148))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #144))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #139))) :mode nil :granularity nil :parent #128) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #139) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #142) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #145))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #140))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #143))) :mode section :granularity nil :parent #140) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #143) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #146) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #149))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #146) #("As root configure the Guix profile\n" 0 35 (:parent #150))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #146)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #146) #("and run for example\n" 0 20 (:parent #152))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #146)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #146) #("If you want to run as root you may have to set\n" 0 47 (:parent #154))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #146)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #146) #("You also need to set\n" 0 21 (:parent #156))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #146)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #146) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #158))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #146) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #159))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #146)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #146) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #161))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #146)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #146) #("When you get errors like:\n" 0 26 (:parent #163))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #146)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #146) #("you may need to set\n" 0 20 (:parent #165))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #144))) :mode nil :granularity nil :parent #140) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #144) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #147) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #150)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #154))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #150) #("s" 0 1 (:parent #155))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #150)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #150) #("plant" 0 5 (:parent #158))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #150))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #147) #("Download one database from\n" 0 27 (:parent #151))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #147) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #147) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #153))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #147)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #147) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #155))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #147)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #147)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #147) #("and\n" 0 4 (:parent #158))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #147)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #147) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #160))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #147)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #147) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #162))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #147) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #163))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #147) #("Note for the plant database you can rename it to db" 0 51 (:parent #164)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #164) #("s" 0 1 (:parent #169))) #(", or\nchange the settings in etc/default" 0 39 (:parent #164)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #164) #("settings.py" 0 11 (:parent #171))) #("to match your path.\n" 0 20 (:parent #164)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #141))) :mode nil :granularity nil :parent #128) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #141) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #144) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #147)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #142))) :mode nil :granularity nil :parent #128) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #142) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #145) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #148))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #145) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #143))) :mode nil :granularity nil :parent #128) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #143) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #146) #("See " 0 4 (:parent #149)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #144))) :mode nil :granularity nil :parent #128) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #144) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #147) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #150)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #150))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #145))) :mode nil :granularity nil :parent #128) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #148) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #151) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #154)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #154) #("PATH" 0 4 (:parent #158))) #("and R" 0 5 (:parent #154)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #154) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #154) #("SITE" 0 4 (:parent #161))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #154))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #151)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #151) #("On one system:\n" 0 15 (:parent #156))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #151)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #151) #("and perhaps a few more.\n" 0 24 (:parent #158))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #149)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #149) #("data" 0 4 (:parent #191))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #149)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #149) #("files" 0 5 (:parent #193))) #("/genotype'" 0 10 (:parent #149))) :mode nil :granularity nil :parent #145) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #149) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #152) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #155)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #155) #("data" 0 4 (:parent #159))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #155)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #155) #("settings.py" 0 11 (:parent #161))) #("(see above in\nthis document).\n" 0 30 (:parent #155))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #152) #("You can use the GENENETWORK" 0 27 (:parent #156)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #156) #("FILES" 0 5 (:parent #160))) #("switch to set the datadir, for example\n" 0 39 (:parent #156))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #150))) :mode nil :granularity nil :parent #145) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #150) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #153) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #156))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #151))) :mode nil :granularity nil :parent #145) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #151) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #154) #("This error\n" 0 11 (:parent #157))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #154)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #154) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #159))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #154) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #160)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #160) #("LIBS" 0 4 (:parent #164))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #160) #("SITE" 0 4 (:parent #165))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #160))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #152))) :mode nil :granularity nil :parent #145) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #152) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #155) #("The following error\n" 0 20 (:parent #158))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #155)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #155) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #160))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #155)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #155) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #162))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #155)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #155) #("if that works run genenetwork after setting SQL" 0 47 (:parent #164)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #164) #("URI" 0 3 (:parent #168))) #("to something like\n" 0 18 (:parent #164))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #155))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #146))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #149) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #152) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #155))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #176) #("add to systemd\n" 0 15 (:parent #179)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #140)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #140) #("Guix-notes" 0 10 (:parent #146))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #140))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #137) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #141) #("Guix bioinformatics" 0 19 (:parent #145))) #("and " 0 4 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #141) #("GNU Guix" 0 8 (:parent #147))) #(".\n" 0 2 (:parent #141))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #137) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #142)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #142) #("GN2 Dependency Graph" 0 20 (:parent #146))) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #135))) :mode nil :granularity nil :parent #129) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #135) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #138) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #141))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #142)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #142)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #142))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #139)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #137))) :mode nil :granularity nil :parent #129) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #137) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #140) #("We run a GNU Guix channel with packages at " 0 43 (:parent #143)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #143) #("guix-bioinformatics" 0 19 (:parent #147))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #143)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #143) #("PACKAGE" 0 7 (:parent #149))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #143) #("PATH" 0 4 (:parent #150))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #143))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #140) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #145))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #140) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #147))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #140)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #140) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #149))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #140)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #140) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #151)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #151) #("substitutes" 0 11 (:parent #155))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #151)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #151)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #151)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\"` switch.\n" 0 11 (:parent #151))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #140) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #152))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #140)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #140) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #154))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #138))) :mode nil :granularity nil :parent #129) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #138) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #141) #("Check out the source with git:\n" 0 31 (:parent #144))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #141) #("Run GN2 with above Guix profile\n" 0 32 (:parent #146))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #141)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #141) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #148))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #141) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #149))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #141) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #150))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #141) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #151))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #141) #("And browse on your local machine to " 0 36 (:parent #152)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #139))) :mode nil :granularity nil :parent #129) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #139) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #142) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #145)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #145) #("README" 0 6 (:parent #149))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #145))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #140))) :mode nil :granularity nil :parent #129) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #140) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #143) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #146))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #141))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #144) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #147) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #150))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #147) #("As root configure the Guix profile\n" 0 35 (:parent #151))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #147)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #147) #("and run for example\n" 0 20 (:parent #153))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #147)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #147) #("If you want to run as root you may have to set\n" 0 47 (:parent #155))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #147) #("You also need to set\n" 0 21 (:parent #157))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #147) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #159))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #147) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #160))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #147) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #162))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #147) #("When you get errors like:\n" 0 26 (:parent #164))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #147) #("you may need to set\n" 0 20 (:parent #166))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #145) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #148) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #151)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #151) #("s" 0 1 (:parent #156))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #151)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #151) #("plant" 0 5 (:parent #159))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #151))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #148) #("Download one database from\n" 0 27 (:parent #152))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #148) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #148) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #154))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #148) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #156))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #148)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #148) #("and\n" 0 4 (:parent #159))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #148) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #161))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #148)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #148) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #163))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #148) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #164))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #148) #("Note for the plant database you can rename it to db" 0 51 (:parent #165)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #165) #("webqtl" 0 6 (:parent #169))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #165) #("s" 0 1 (:parent #170))) #(", or\nchange the settings in etc/default" 0 39 (:parent #165)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #165) #("settings.py" 0 11 (:parent #172))) #("to match your path.\n" 0 20 (:parent #165)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #142))) :mode nil :granularity nil :parent #129) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #142) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #145) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #148)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #143))) :mode nil :granularity nil :parent #129) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #143) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #146) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #149))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #146) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #144))) :mode nil :granularity nil :parent #129) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #144) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #147) #("See " 0 4 (:parent #150)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #145))) :mode nil :granularity nil :parent #129) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #145) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #148) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #151)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #151))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #146))) :mode nil :granularity nil :parent #129) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #149) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #152) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #155)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #155) #("PATH" 0 4 (:parent #159))) #("and R" 0 5 (:parent #155)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #155) #("LIBS" 0 4 (:parent #161))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #155) #("SITE" 0 4 (:parent #162))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #155))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #152)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #152) #("On one system:\n" 0 15 (:parent #157))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #152)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #152) #("and perhaps a few more.\n" 0 24 (:parent #159))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #150)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #150) #("data" 0 4 (:parent #192))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #150)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #150) #("files" 0 5 (:parent #194))) #("/genotype'" 0 10 (:parent #150))) :mode nil :granularity nil :parent #146) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #150) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #153) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #156)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #156) #("data" 0 4 (:parent #160))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #156)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #156) #("settings.py" 0 11 (:parent #162))) #("(see above in\nthis document).\n" 0 30 (:parent #156))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #153) #("You can use the GENENETWORK" 0 27 (:parent #157)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #157) #("FILES" 0 5 (:parent #161))) #("switch to set the datadir, for example\n" 0 39 (:parent #157))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #151) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #154) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #157))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #152) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #155) #("This error\n" 0 11 (:parent #158))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #155)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #155) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #160))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #155) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #161)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #161) #("LIBS" 0 4 (:parent #165))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #161) #("SITE" 0 4 (:parent #166))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #161))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #153) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #156) #("The following error\n" 0 20 (:parent #159))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #156)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #156) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #161))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #156)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #156) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #163))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #156)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #156) #("if that works run genenetwork after setting SQL" 0 47 (:parent #165)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #165) #("URI" 0 3 (:parent #169))) #("to something like\n" 0 18 (:parent #165))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #156))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #147))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #150) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #153) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #156))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #177) #("add to systemd\n" 0 15 (:parent #180)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #141) #("Guix-notes" 0 10 (:parent #147))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #141))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #138) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #142) #("Guix bioinformatics" 0 19 (:parent #146))) #("and " 0 4 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #142) #("GNU Guix" 0 8 (:parent #148))) #(".\n" 0 2 (:parent #142))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #138) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #143)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #143) #("GN2 Dependency Graph" 0 20 (:parent #147))) #(".\n" 0 2 (:parent #143))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #136))) :mode nil :granularity nil :parent #130) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #136) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #139) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #142))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #143)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #143)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #143))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #138))) :mode nil :granularity nil :parent #130) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #138) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #141) #("We run a GNU Guix channel with packages at " 0 43 (:parent #144)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #144) #("guix-bioinformatics" 0 19 (:parent #148))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #144)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #144) #("PACKAGE" 0 7 (:parent #150))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #144) #("PATH" 0 4 (:parent #151))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #144))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #141) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #146))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #141) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #148))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #141)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #141) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #150))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #141) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #152)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #152) #("substitutes" 0 11 (:parent #156))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #152)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\"` switch.\n" 0 11 (:parent #152))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #141) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #153))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #141)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #141) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #155))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #139))) :mode nil :granularity nil :parent #130) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #139) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #142) #("Check out the source with git:\n" 0 31 (:parent #145))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #142)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #142) #("Run GN2 with above Guix profile\n" 0 32 (:parent #147))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #142)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #142) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #149))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #142) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #150))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #142) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #151))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #142) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #152))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #142) #("And browse on your local machine to " 0 36 (:parent #153)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #140))) :mode nil :granularity nil :parent #130) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #140) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #143) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #146)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #146) #("README" 0 6 (:parent #150))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #146))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #141))) :mode nil :granularity nil :parent #130) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #141) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #144) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #147))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #142))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #145) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #148) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #151))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #148) #("As root configure the Guix profile\n" 0 35 (:parent #152))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #148)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #148) #("and run for example\n" 0 20 (:parent #154))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #148)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #148) #("If you want to run as root you may have to set\n" 0 47 (:parent #156))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #148) #("You also need to set\n" 0 21 (:parent #158))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #148) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #160))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #148) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #161))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #148) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #163))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #148) #("When you get errors like:\n" 0 26 (:parent #165))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #148) #("you may need to set\n" 0 20 (:parent #167))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #146))) :mode nil :granularity nil :parent #142) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #146) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #149) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #152)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #152) #("s" 0 1 (:parent #157))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #152)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #159))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #152) #("plant" 0 5 (:parent #160))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #152))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #149) #("Download one database from\n" 0 27 (:parent #153))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #149) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #149) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #155))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #149) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #157))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #149)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #149) #("and\n" 0 4 (:parent #160))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #149) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #162))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #149)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #149) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #164))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #149) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #165))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #149) #("Note for the plant database you can rename it to db" 0 51 (:parent #166)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #170))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #166) #("s" 0 1 (:parent #171))) #(", or\nchange the settings in etc/default" 0 39 (:parent #166)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #166) #("settings.py" 0 11 (:parent #173))) #("to match your path.\n" 0 20 (:parent #166)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #143))) :mode nil :granularity nil :parent #130) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #143) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #146) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #149)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #144))) :mode nil :granularity nil :parent #130) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #144) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #147) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #150))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #147) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #145))) :mode nil :granularity nil :parent #130) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #145) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #148) #("See " 0 4 (:parent #151)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(".\n" 0 2 (:parent #151))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #146))) :mode nil :granularity nil :parent #130) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #146) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #149) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #152)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #152))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #147))) :mode nil :granularity nil :parent #130) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #150) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #153) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #156)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #156) #("PATH" 0 4 (:parent #160))) #("and R" 0 5 (:parent #156)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #156) #("SITE" 0 4 (:parent #163))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #156))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #153)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #153) #("On one system:\n" 0 15 (:parent #158))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #153)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #153) #("and perhaps a few more.\n" 0 24 (:parent #160))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #151)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #151) #("data" 0 4 (:parent #193))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #151)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #151) #("files" 0 5 (:parent #195))) #("/genotype'" 0 10 (:parent #151))) :mode nil :granularity nil :parent #147) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #151) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #154) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #157)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #157) #("data" 0 4 (:parent #161))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #157)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #157) #("settings.py" 0 11 (:parent #163))) #("(see above in\nthis document).\n" 0 30 (:parent #157))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #154) #("You can use the GENENETWORK" 0 27 (:parent #158)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #158) #("FILES" 0 5 (:parent #162))) #("switch to set the datadir, for example\n" 0 39 (:parent #158))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #152) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #155) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #158))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #153) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #156) #("This error\n" 0 11 (:parent #159))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #156)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #156) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #161))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #156) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #162)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #162) #("LIBS" 0 4 (:parent #166))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #162) #("SITE" 0 4 (:parent #167))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #162))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #154) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #157) #("The following error\n" 0 20 (:parent #160))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #157)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #157) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #162))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #157)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #157) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #164))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #157)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #157) #("if that works run genenetwork after setting SQL" 0 47 (:parent #166)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #166) #("URI" 0 3 (:parent #170))) #("to something like\n" 0 18 (:parent #166))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #157))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #148))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #151) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #154) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #157))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #178) #("add to systemd\n" 0 15 (:parent #181)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #142)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #142) #("Guix-notes" 0 10 (:parent #148))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #142))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #139) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #143) #("Guix bioinformatics" 0 19 (:parent #147))) #("and " 0 4 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #143) #("GNU Guix" 0 8 (:parent #149))) #(".\n" 0 2 (:parent #143))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #139) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #144)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #144) #("GN2 Dependency Graph" 0 20 (:parent #148))) #(".\n" 0 2 (:parent #144))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #137))) :mode nil :granularity nil :parent #131) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #137) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #140) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #143))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #144)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #144)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #144))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #141)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #139))) :mode nil :granularity nil :parent #131) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #139) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #142) #("We run a GNU Guix channel with packages at " 0 43 (:parent #145)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #145) #("guix-bioinformatics" 0 19 (:parent #149))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #145)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #145) #("PACKAGE" 0 7 (:parent #151))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #145) #("PATH" 0 4 (:parent #152))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #145))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #142) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #147))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #142) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #149))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #142) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #151))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #142) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #153)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #153) #("substitutes" 0 11 (:parent #157))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #153)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\"` switch.\n" 0 11 (:parent #153))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #142) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #154))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #142) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #156))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #140))) :mode nil :granularity nil :parent #131) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #140) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #143) #("Check out the source with git:\n" 0 31 (:parent #146))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #143) #("Run GN2 with above Guix profile\n" 0 32 (:parent #148))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #143) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #150))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #143) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #151))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #143) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #152))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #143) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #153))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #143) #("And browse on your local machine to " 0 36 (:parent #154)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #141))) :mode nil :granularity nil :parent #131) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #141) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #144) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #147)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #147) #("README" 0 6 (:parent #151))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #147))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #142))) :mode nil :granularity nil :parent #131) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #142) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #145) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #148))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #143))) :mode nil :granularity nil :parent #131) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #146) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #149) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #152))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #149) #("As root configure the Guix profile\n" 0 35 (:parent #153))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #149)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #149) #("and run for example\n" 0 20 (:parent #155))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #149)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #149) #("If you want to run as root you may have to set\n" 0 47 (:parent #157))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #149) #("You also need to set\n" 0 21 (:parent #159))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #149) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #161))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #149) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #162))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #149) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #164))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #149) #("When you get errors like:\n" 0 26 (:parent #166))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #149) #("you may need to set\n" 0 20 (:parent #168))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #147) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #150) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #153)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #153) #("s" 0 1 (:parent #158))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #153)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #160))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #153) #("plant" 0 5 (:parent #161))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #153))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #150) #("Download one database from\n" 0 27 (:parent #154))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #150) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #150) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #156))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #150) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #158))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #150)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #150) #("and\n" 0 4 (:parent #161))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #150) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #163))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #150) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #165))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #150) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #166))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #150) #("Note for the plant database you can rename it to db" 0 51 (:parent #167)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #167) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #167) #("s" 0 1 (:parent #172))) #(", or\nchange the settings in etc/default" 0 39 (:parent #167)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #167) #("settings.py" 0 11 (:parent #174))) #("to match your path.\n" 0 20 (:parent #167)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #144))) :mode nil :granularity nil :parent #131) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #144) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #147) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #150)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #145))) :mode nil :granularity nil :parent #131) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #145) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #148) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #151))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #148) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #146))) :mode nil :granularity nil :parent #131) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #146) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #149) #("See " 0 4 (:parent #152)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(".\n" 0 2 (:parent #152))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #147))) :mode nil :granularity nil :parent #131) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #147) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #150) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #153)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #153))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #148))) :mode nil :granularity nil :parent #131) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #151) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #154) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #157)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #157) #("PATH" 0 4 (:parent #161))) #("and R" 0 5 (:parent #157)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #157) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #157) #("SITE" 0 4 (:parent #164))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #157))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #154)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #154) #("On one system:\n" 0 15 (:parent #159))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #154)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #154) #("and perhaps a few more.\n" 0 24 (:parent #161))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #152)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #152) #("data" 0 4 (:parent #194))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #152)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #152) #("files" 0 5 (:parent #196))) #("/genotype'" 0 10 (:parent #152))) :mode nil :granularity nil :parent #148) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #152) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #155) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #158)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #158) #("data" 0 4 (:parent #162))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #158)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #158) #("settings.py" 0 11 (:parent #164))) #("(see above in\nthis document).\n" 0 30 (:parent #158))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #155) #("You can use the GENENETWORK" 0 27 (:parent #159)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #159) #("FILES" 0 5 (:parent #163))) #("switch to set the datadir, for example\n" 0 39 (:parent #159))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #155)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #153))) :mode nil :granularity nil :parent #148) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #153) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #156) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #159))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #154))) :mode nil :granularity nil :parent #148) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #154) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #157) #("This error\n" 0 11 (:parent #160))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #157)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #157) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #162))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #157) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #163)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #163) #("LIBS" 0 4 (:parent #167))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #163) #("SITE" 0 4 (:parent #168))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #163))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #155))) :mode nil :granularity nil :parent #148) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #155) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #158) #("The following error\n" 0 20 (:parent #161))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #158)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #158) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #163))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #158)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #158) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #165))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #158)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #158) #("if that works run genenetwork after setting SQL" 0 47 (:parent #167)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #167) #("URI" 0 3 (:parent #171))) #("to something like\n" 0 18 (:parent #167))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #158))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #149))) :mode nil :granularity nil :parent #131) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #152))) :mode section :granularity nil :parent #149) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #152) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #155) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #158))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #179) #("add to systemd\n" 0 15 (:parent #182)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #143)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #143) #("Guix-notes" 0 10 (:parent #149))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #143))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #140) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #144) #("Guix bioinformatics" 0 19 (:parent #148))) #("and " 0 4 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #144) #("GNU Guix" 0 8 (:parent #150))) #(".\n" 0 2 (:parent #144))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #140) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #145)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #145) #("GN2 Dependency Graph" 0 20 (:parent #149))) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #138))) :mode nil :granularity nil :parent #132) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #138) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #141) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #144))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Debian-derived distros\nmay support\n" 0 117 (:parent #145))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #140))) :mode nil :granularity nil :parent #132) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #140) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #143) #("We run a GNU Guix channel with packages at " 0 43 (:parent #146)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #146) #("guix-bioinformatics" 0 19 (:parent #150))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #146)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #146) #("PACKAGE" 0 7 (:parent #152))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #146) #("PATH" 0 4 (:parent #153))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #146))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #143) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #148))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #143) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #150))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #143) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #152))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #143) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #154)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #154) #("substitutes" 0 11 (:parent #158))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #154)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #154)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #154)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\"` switch.\n" 0 11 (:parent #154))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #143) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #155))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #143) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #157))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #141))) :mode nil :granularity nil :parent #132) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #141) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #144) #("Check out the source with git:\n" 0 31 (:parent #147))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #144) #("Run GN2 with above Guix profile\n" 0 32 (:parent #149))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #144) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #151))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #144) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #152))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #144) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #153))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #144) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #154))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #144) #("And browse on your local machine to " 0 36 (:parent #155)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #142))) :mode nil :granularity nil :parent #132) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #142) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #145) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #148)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #148) #("README" 0 6 (:parent #152))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #148))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #143))) :mode nil :granularity nil :parent #132) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #143) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #146) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #149))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #144))) :mode nil :granularity nil :parent #132) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #147) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #150) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #153))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #150) #("As root configure the Guix profile\n" 0 35 (:parent #154))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #150)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #150) #("and run for example\n" 0 20 (:parent #156))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #150)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #150) #("If you want to run as root you may have to set\n" 0 47 (:parent #158))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #150) #("You also need to set\n" 0 21 (:parent #160))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #150) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #162))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #150) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #163))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #150) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #165))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #150) #("When you get errors like:\n" 0 26 (:parent #167))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #150) #("you may need to set\n" 0 20 (:parent #169))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #148) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #151) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #154)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #154) #("s" 0 1 (:parent #159))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #154)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #161))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #154) #("plant" 0 5 (:parent #162))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #154))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #151) #("Download one database from\n" 0 27 (:parent #155))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #151) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #151) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #157))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #151) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #159))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #151)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #151) #("and\n" 0 4 (:parent #162))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #151) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #164))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #151) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #166))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #151) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #167))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #151) #("Note for the plant database you can rename it to db" 0 51 (:parent #168)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #168) #("s" 0 1 (:parent #173))) #(", or\nchange the settings in etc/default" 0 39 (:parent #168)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #168) #("settings.py" 0 11 (:parent #175))) #("to match your path.\n" 0 20 (:parent #168)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #145))) :mode nil :granularity nil :parent #132) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #145) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #148) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #151)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #146))) :mode nil :granularity nil :parent #132) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #146) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #149) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #152))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #149) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #147))) :mode nil :granularity nil :parent #132) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #147) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #150) #("See " 0 4 (:parent #153)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #(".\n" 0 2 (:parent #153))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #148))) :mode nil :granularity nil :parent #132) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #148) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #151) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #154)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #154))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #149))) :mode nil :granularity nil :parent #132) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #152))) :mode section :granularity nil :parent #149) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #152) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #155) #("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 #158)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #158) #("PATH" 0 4 (:parent #162))) #("and R" 0 5 (:parent #158)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #164))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #158) #("SITE" 0 4 (:parent #165))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #158))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #155)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #155) #("On one system:\n" 0 15 (:parent #160))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #155)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #155) #("and perhaps a few more.\n" 0 24 (:parent #162))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #153)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #153) #("data" 0 4 (:parent #195))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #153)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #153) #("files" 0 5 (:parent #197))) #("/genotype'" 0 10 (:parent #153))) :mode nil :granularity nil :parent #149) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #153) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #156) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #159)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #159) #("data" 0 4 (:parent #163))) #(". 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 #159)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #159) #("settings.py" 0 11 (:parent #165))) #("(see above in\nthis document).\n" 0 30 (:parent #159))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #156) #("You can use the GENENETWORK" 0 27 (:parent #160)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #160) #("FILES" 0 5 (:parent #164))) #("switch to set the datadir, for example\n" 0 39 (:parent #160))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #154))) :mode nil :granularity nil :parent #149) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #154) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #157) #("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 #160))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #155))) :mode nil :granularity nil :parent #149) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #155) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #158) #("This error\n" 0 11 (:parent #161))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #158)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #158) #("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 #163))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #158) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #164)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #164) #("LIBS" 0 4 (:parent #168))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #164) #("SITE" 0 4 (:parent #169))) #(". 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 #164))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #156))) :mode nil :granularity nil :parent #149) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #156) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #159) #("The following error\n" 0 20 (:parent #162))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #159)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #159) #("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 #164))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #159)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #159) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #166))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #159)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #159) #("if that works run genenetwork after setting SQL" 0 47 (:parent #168)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #168) #("URI" 0 3 (:parent #172))) #("to something like\n" 0 18 (:parent #168))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #159))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #150))) :mode nil :granularity nil :parent #132) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #153))) :mode section :granularity nil :parent #150) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #153) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #156) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #159))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #180) #("add to systemd\n" 0 15 (:parent #183)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #144)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #144) #("Guix-notes" 0 10 (:parent #150))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #144))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #141) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #145) #("Guix bioinformatics" 0 19 (:parent #149))) #("and " 0 4 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #145) #("GNU Guix" 0 8 (:parent #151))) #(".\n" 0 2 (:parent #145))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #141) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #146)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #146) #("GN2 Dependency Graph" 0 20 (:parent #150))) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #139))) :mode nil :granularity nil :parent #133) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #139) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #142) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #145))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #146)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #146)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #146))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #143)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #141))) :mode nil :granularity nil :parent #133) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #141) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #144) #("We run a GNU Guix channel with packages at " 0 43 (:parent #147)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #147) #("guix-bioinformatics" 0 19 (:parent #151))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #147)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #147) #("PACKAGE" 0 7 (:parent #153))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #147) #("PATH" 0 4 (:parent #154))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #147))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #144) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #149))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #144) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #151))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #144) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #153))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #144) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #155)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #155) #("substitutes" 0 11 (:parent #159))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #155)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #155)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #155)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\"` switch.\n" 0 11 (:parent #155))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #144) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #156))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #144) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #158))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #142))) :mode nil :granularity nil :parent #133) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #142) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #145) #("Check out the source with git:\n" 0 31 (:parent #148))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #145) #("Run GN2 with above Guix profile\n" 0 32 (:parent #150))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #145) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #152))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #145) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #153))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #145) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #154))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #145) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #155))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #145) #("And browse on your local machine to " 0 36 (:parent #156)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #143))) :mode nil :granularity nil :parent #133) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #143) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #146) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #149)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #149) #("README" 0 6 (:parent #153))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #149))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #144))) :mode nil :granularity nil :parent #133) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #144) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #147) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #150))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #145))) :mode nil :granularity nil :parent #133) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #148) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #151) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #154))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #151) #("As root configure the Guix profile\n" 0 35 (:parent #155))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #151)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #151) #("and run for example\n" 0 20 (:parent #157))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #151)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #151) #("If you want to run as root you may have to set\n" 0 47 (:parent #159))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #151) #("You also need to set\n" 0 21 (:parent #161))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #151) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #163))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #151) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #164))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #151) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #166))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #151) #("When you get errors like:\n" 0 26 (:parent #168))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #151) #("you may need to set\n" 0 20 (:parent #170))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #149))) :mode nil :granularity nil :parent #145) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #149) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #152) #("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 #155)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #155) #("webqtl" 0 6 (:parent #159))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #155) #("s" 0 1 (:parent #160))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #155)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #155) #("webqtl" 0 6 (:parent #162))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #155) #("plant" 0 5 (:parent #163))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #155))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #152) #("Download one database from\n" 0 27 (:parent #156))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #152) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #152) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #158))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #152) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #160))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #152)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #152) #("and\n" 0 4 (:parent #163))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #152) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #165))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #152) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #167))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #152) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #168))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #152) #("Note for the plant database you can rename it to db" 0 51 (:parent #169)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #(", or\nchange the settings in etc/default" 0 39 (:parent #169)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #169) #("settings.py" 0 11 (:parent #176))) #("to match your path.\n" 0 20 (:parent #169)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #146))) :mode nil :granularity nil :parent #133) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #146) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #149) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #152)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #147))) :mode nil :granularity nil :parent #133) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #147) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #150) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #153))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #150) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #148))) :mode nil :granularity nil :parent #133) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #148) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #151) #("See " 0 4 (:parent #154)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #(".\n" 0 2 (:parent #154))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #149))) :mode nil :granularity nil :parent #133) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #149) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #152) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #155)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #155))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #150))) :mode nil :granularity nil :parent #133) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #153))) :mode section :granularity nil :parent #150) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #153) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #156) #("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 #159)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #159) #("PATH" 0 4 (:parent #163))) #("and R" 0 5 (:parent #159)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #159) #("LIBS" 0 4 (:parent #165))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #159) #("SITE" 0 4 (:parent #166))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #159))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #156)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #156) #("On one system:\n" 0 15 (:parent #161))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #156)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #156) #("and perhaps a few more.\n" 0 24 (:parent #163))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #154)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #154) #("data" 0 4 (:parent #196))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #154)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #154) #("files" 0 5 (:parent #198))) #("/genotype'" 0 10 (:parent #154))) :mode nil :granularity nil :parent #150) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #154) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #157) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #160)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #160) #("data" 0 4 (:parent #164))) #(". 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 #160)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #160) #("settings.py" 0 11 (:parent #166))) #("(see above in\nthis document).\n" 0 30 (:parent #160))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #157) #("You can use the GENENETWORK" 0 27 (:parent #161)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #161) #("FILES" 0 5 (:parent #165))) #("switch to set the datadir, for example\n" 0 39 (:parent #161))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #157)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #155))) :mode nil :granularity nil :parent #150) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #155) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #158) #("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 #161))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #156))) :mode nil :granularity nil :parent #150) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #156) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #159) #("This error\n" 0 11 (:parent #162))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #159)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #159) #("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 #164))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #159) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #165)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #165) #("LIBS" 0 4 (:parent #169))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #165) #("SITE" 0 4 (:parent #170))) #(". 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 #165))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #157))) :mode nil :granularity nil :parent #150) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #157) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #160) #("The following error\n" 0 20 (:parent #163))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #160)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #160) #("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 #165))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #160)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #160) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #167))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #160)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #160) #("if that works run genenetwork after setting SQL" 0 47 (:parent #169)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #169) #("URI" 0 3 (:parent #173))) #("to something like\n" 0 18 (:parent #169))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #160))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #151))) :mode nil :granularity nil :parent #133) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #154))) :mode section :granularity nil :parent #151) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #154) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #157) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #160))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #181) #("add to systemd\n" 0 15 (:parent #184)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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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 #145)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #145) #("Guix-notes" 0 10 (:parent #151))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #145))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #142) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #146) #("Guix bioinformatics" 0 19 (:parent #150))) #("and " 0 4 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #146) #("GNU Guix" 0 8 (:parent #152))) #(".\n" 0 2 (:parent #146))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #142) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #147)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #147) #("GN2 Dependency Graph" 0 20 (:parent #151))) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #140))) :mode nil :granularity nil :parent #134) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #140) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #143) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #146))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #147)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #147)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #147))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #142))) :mode nil :granularity nil :parent #134) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #142) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #145) #("We run a GNU Guix channel with packages at " 0 43 (:parent #148)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #148) #("guix-bioinformatics" 0 19 (:parent #152))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #148)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #148) #("PACKAGE" 0 7 (:parent #154))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #148) #("PATH" 0 4 (:parent #155))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #148))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #145) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #150))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #145) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #152))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #145) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #154))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #145) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #156)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #156) #("substitutes" 0 11 (:parent #160))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #156)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #156)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #156)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\"` switch.\n" 0 11 (:parent #156))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #145) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #157))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #145) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #159))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #143))) :mode nil :granularity nil :parent #134) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #143) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #146) #("Check out the source with git:\n" 0 31 (:parent #149))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #146) #("Run GN2 with above Guix profile\n" 0 32 (:parent #151))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #146) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #153))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #146) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #154))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #146) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #155))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #146) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #156))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #146) #("And browse on your local machine to " 0 36 (:parent #157)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #144))) :mode nil :granularity nil :parent #134) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #144) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #147) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #150)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #150) #("README" 0 6 (:parent #154))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #150))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #145))) :mode nil :granularity nil :parent #134) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #145) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #148) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #151))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #146))) :mode nil :granularity nil :parent #134) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #149) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #152) #("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 #155))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #152) #("As root configure the Guix profile\n" 0 35 (:parent #156))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #152)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #152) #("and run for example\n" 0 20 (:parent #158))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #152)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #152) #("If you want to run as root you may have to set\n" 0 47 (:parent #160))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #152) #("You also need to set\n" 0 21 (:parent #162))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #152) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #164))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #152) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #165))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #152) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #167))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #152) #("When you get errors like:\n" 0 26 (:parent #169))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #152) #("you may need to set\n" 0 20 (:parent #171))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #150))) :mode nil :granularity nil :parent #146) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #150) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #153) #("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 #156)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #156) #("webqtl" 0 6 (:parent #160))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #156) #("s" 0 1 (:parent #161))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #156)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #156) #("webqtl" 0 6 (:parent #163))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #156) #("plant" 0 5 (:parent #164))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #156))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #153) #("Download one database from\n" 0 27 (:parent #157))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #153) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n" 0 1 (:parent #158))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #153) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #159))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #153) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #161))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #153)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #153) #("and\n" 0 4 (:parent #164))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #153) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #166))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #153) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #168))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #153) #("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 #169))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #153) #("Note for the plant database you can rename it to db" 0 51 (:parent #170)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #170) #("webqtl" 0 6 (:parent #174))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #170) #("s" 0 1 (:parent #175))) #(", or\nchange the settings in etc/default" 0 39 (:parent #170)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #170) #("settings.py" 0 11 (:parent #177))) #("to match your path.\n" 0 20 (:parent #170)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #147))) :mode nil :granularity nil :parent #134) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #147) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #150) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #153)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #148))) :mode nil :granularity nil :parent #134) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #148) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #151) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #154))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #151) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #149))) :mode nil :granularity nil :parent #134) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #149) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #152) #("See " 0 4 (:parent #155)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #(".\n" 0 2 (:parent #155))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #150))) :mode nil :granularity nil :parent #134) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #150) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #153) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #156)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #156))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #151))) :mode nil :granularity nil :parent #134) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #154))) :mode section :granularity nil :parent #151) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #154) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #157) #("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 #160)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #160) #("PATH" 0 4 (:parent #164))) #("and R" 0 5 (:parent #160)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #160) #("LIBS" 0 4 (:parent #166))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #160) #("SITE" 0 4 (:parent #167))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #160))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #157)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #157) #("On one system:\n" 0 15 (:parent #162))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #157)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #157) #("and perhaps a few more.\n" 0 24 (:parent #164))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #155)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #155) #("data" 0 4 (:parent #197))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #155)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #155) #("files" 0 5 (:parent #199))) #("/genotype'" 0 10 (:parent #155))) :mode nil :granularity nil :parent #151) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #155) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #158) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #161)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #161) #("data" 0 4 (:parent #165))) #(". 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 #161)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #161) #("settings.py" 0 11 (:parent #167))) #("(see above in\nthis document).\n" 0 30 (:parent #161))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #158) #("You can use the GENENETWORK" 0 27 (:parent #162)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #162) #("FILES" 0 5 (:parent #166))) #("switch to set the datadir, for example\n" 0 39 (:parent #162))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #158)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #156) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #159) #("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 #162))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #157) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #160) #("This error\n" 0 11 (:parent #163))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #160)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #160) #("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 #165))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #160) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #166)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #166) #("LIBS" 0 4 (:parent #170))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #166) #("SITE" 0 4 (:parent #171))) #(". 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 #166))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #158) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #161) #("The following error\n" 0 20 (:parent #164))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #161)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #161) #("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 #166))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #161)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #161) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #168))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #161)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #161) #("if that works run genenetwork after setting SQL" 0 47 (:parent #170)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #170) #("URI" 0 3 (:parent #174))) #("to something like\n" 0 18 (:parent #170))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #161))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #152))) :mode nil :granularity nil :parent #134) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #155) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #158) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #161))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #182) #("add to systemd\n" 0 15 (:parent #185)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #148) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #156) #("Mariadb\n" 0 8 (:parent #159))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #142))) :mode nil :granularity nil :parent #135) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #142) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #145) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #148)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #148))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #143))) :mode nil :granularity nil :parent #135) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #143) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #146) #("We run a GNU Guix channel with packages at " 0 43 (:parent #149)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #149) #("guix-bioinformatics" 0 19 (:parent #153))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #149)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #149) #("PACKAGE" 0 7 (:parent #155))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #149) #("PATH" 0 4 (:parent #156))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #149))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #146) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #151))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #146) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #153))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #146) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #155))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #146) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #157)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #157) #("substitutes" 0 11 (:parent #161))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #157)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #157)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #157)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\"` switch.\n" 0 11 (:parent #157))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #146) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #158))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #146) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #160))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #144))) :mode nil :granularity nil :parent #135) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #144) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #147) #("Check out the source with git:\n" 0 31 (:parent #150))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #147) #("Run GN2 with above Guix profile\n" 0 32 (:parent #152))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #147) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #154))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #147) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #155))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #147) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #156))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #147) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #157))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #147) #("And browse on your local machine to " 0 36 (:parent #158)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n" 0 1 (:parent #158))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #145))) :mode nil :granularity nil :parent #135) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #145) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #148) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #151)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #151) #("README" 0 6 (:parent #155))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #151))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #146))) :mode nil :granularity nil :parent #135) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #146) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #149) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #152))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #147))) :mode nil :granularity nil :parent #135) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #150) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #153) #("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 #156))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #153) #("As root configure the Guix profile\n" 0 35 (:parent #157))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #153)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #153) #("and run for example\n" 0 20 (:parent #159))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #153)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #153) #("If you want to run as root you may have to set\n" 0 47 (:parent #161))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #153) #("You also need to set\n" 0 21 (:parent #163))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #153) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #165))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #153) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #166))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #153) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #168))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #153) #("When you get errors like:\n" 0 26 (:parent #170))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #153) #("you may need to set\n" 0 20 (:parent #172))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #151))) :mode nil :granularity nil :parent #147) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #151) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #154) #("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 #157)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #157) #("webqtl" 0 6 (:parent #161))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #157) #("s" 0 1 (:parent #162))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #157)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #157) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #157) #("plant" 0 5 (:parent #165))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #157))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #154) #("Download one database from\n" 0 27 (:parent #158))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #154) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n" 0 1 (:parent #159))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #154) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #160))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #154) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #162))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #154)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #154) #("and\n" 0 4 (:parent #165))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #154) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #167))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #154) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #169))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #154) #("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 #170))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #154) #("Note for the plant database you can rename it to db" 0 51 (:parent #171)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #171) #("webqtl" 0 6 (:parent #175))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #171) #("s" 0 1 (:parent #176))) #(", or\nchange the settings in etc/default" 0 39 (:parent #171)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #171) #("settings.py" 0 11 (:parent #178))) #("to match your path.\n" 0 20 (:parent #171)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #148))) :mode nil :granularity nil :parent #135) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #148) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #151) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #154)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #149))) :mode nil :granularity nil :parent #135) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #149) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #152) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #155))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #152) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #150))) :mode nil :granularity nil :parent #135) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #150) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #153) #("See " 0 4 (:parent #156)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #(".\n" 0 2 (:parent #156))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #151))) :mode nil :granularity nil :parent #135) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #151) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #154) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #157)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #157))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #152))) :mode nil :granularity nil :parent #135) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #155) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #158) #("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 #161)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #161) #("PATH" 0 4 (:parent #165))) #("and R" 0 5 (:parent #161)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #161) #("LIBS" 0 4 (:parent #167))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #161) #("SITE" 0 4 (:parent #168))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #161))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #158)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #158) #("On one system:\n" 0 15 (:parent #163))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #158)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #158) #("and perhaps a few more.\n" 0 24 (:parent #165))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #156)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #156) #("data" 0 4 (:parent #198))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #156)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #156) #("files" 0 5 (:parent #200))) #("/genotype'" 0 10 (:parent #156))) :mode nil :granularity nil :parent #152) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #156) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #159) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #162)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #162) #("data" 0 4 (:parent #166))) #(". 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 #162)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #168))) #("(see above in\nthis document).\n" 0 30 (:parent #162))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #159) #("You can use the GENENETWORK" 0 27 (:parent #163)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #163) #("FILES" 0 5 (:parent #167))) #("switch to set the datadir, for example\n" 0 39 (:parent #163))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #159)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #157))) :mode nil :granularity nil :parent #152) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #157) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #160) #("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 #163))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #158))) :mode nil :granularity nil :parent #152) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #158) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #161) #("This error\n" 0 11 (:parent #164))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #161)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #161) #("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 #166))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #161) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #167)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #167) #("LIBS" 0 4 (:parent #171))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #167) #("SITE" 0 4 (:parent #172))) #(". 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 #167))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #159))) :mode nil :granularity nil :parent #152) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #159) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #162) #("The following error\n" 0 20 (:parent #165))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #162)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #162) #("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 #167))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #162)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #162) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #169))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #162)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #162) #("if that works run genenetwork after setting SQL" 0 47 (:parent #171)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #171) #("URI" 0 3 (:parent #175))) #("to something like\n" 0 18 (:parent #171))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #162))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #153))) :mode nil :granularity nil :parent #135) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #156))) :mode section :granularity nil :parent #153) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #156) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #159) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #162))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #182) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #185)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #185)) #("\n" 0 1 (:parent #185)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #170) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #175) #("Create a gn2 user and home with space\n" 0 38 (:parent #178)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#176) #("Install redis\n" 0 14 (:parent #179))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #176) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #183) #("add to systemd\n" 0 15 (:parent #186)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #180) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #184) #("update redis.cnf\n" 0 17 (:parent #187)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #180) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #185) #("update database\n" 0 16 (:parent #188)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #147)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #147) #("Guix-notes" 0 10 (:parent #153))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #147))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #144) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #148) #("Guix bioinformatics" 0 19 (:parent #152))) #("and " 0 4 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #148) #("GNU Guix" 0 8 (:parent #154))) #(".\n" 0 2 (:parent #148))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #144) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #149)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #149) #("GN2 Dependency Graph" 0 20 (:parent #153))) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #142))) :mode nil :granularity nil :parent #136) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #142) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #145) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #148))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #149) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #157) #("Mariadb\n" 0 8 (:parent #160))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #143))) :mode nil :granularity nil :parent #136) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #143) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #146) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #149)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #149)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #149))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #144))) :mode nil :granularity nil :parent #136) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #144) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #147) #("We run a GNU Guix channel with packages at " 0 43 (:parent #150)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #150) #("guix-bioinformatics" 0 19 (:parent #154))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #150)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #150) #("PACKAGE" 0 7 (:parent #156))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #150) #("PATH" 0 4 (:parent #157))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #150))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #147) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #152))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #147) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #154))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #147) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #156))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #147) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #158)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #158) #("substitutes" 0 11 (:parent #162))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #158)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\"` switch.\n" 0 11 (:parent #158))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #147) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #159))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #147) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #161))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #145))) :mode nil :granularity nil :parent #136) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #145) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #148) #("Check out the source with git:\n" 0 31 (:parent #151))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #148) #("Run GN2 with above Guix profile\n" 0 32 (:parent #153))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #148) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #155))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #148) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #156))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #148) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #157))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #148) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #158))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #148) #("And browse on your local machine to " 0 36 (:parent #159)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n" 0 1 (:parent #159))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #146))) :mode nil :granularity nil :parent #136) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #146) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #149) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #152)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #152) #("README" 0 6 (:parent #156))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #152))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #147))) :mode nil :granularity nil :parent #136) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #147) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #150) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #153))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #148))) :mode nil :granularity nil :parent #136) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #151) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #154) #("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 #157))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #154) #("As root configure the Guix profile\n" 0 35 (:parent #158))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #154)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #154) #("and run for example\n" 0 20 (:parent #160))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #154)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #154) #("If you want to run as root you may have to set\n" 0 47 (:parent #162))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #154) #("You also need to set\n" 0 21 (:parent #164))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #154) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #166))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #154) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #167))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #154) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #169))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #154) #("When you get errors like:\n" 0 26 (:parent #171))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #154) #("you may need to set\n" 0 20 (:parent #173))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #152))) :mode nil :granularity nil :parent #148) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #152) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #155) #("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 #158)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #158) #("webqtl" 0 6 (:parent #162))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #158) #("s" 0 1 (:parent #163))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #158)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #158) #("webqtl" 0 6 (:parent #165))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #158) #("plant" 0 5 (:parent #166))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #158))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #155) #("Download one database from\n" 0 27 (:parent #159))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #155) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n" 0 1 (:parent #160))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #155) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #161))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #155) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #163))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #155)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #155) #("and\n" 0 4 (:parent #166))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #155) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #168))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #155) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #170))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #155) #("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 #171))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #155) #("Note for the plant database you can rename it to db" 0 51 (:parent #172)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #172) #("webqtl" 0 6 (:parent #176))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #172) #("s" 0 1 (:parent #177))) #(", or\nchange the settings in etc/default" 0 39 (:parent #172)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #172) #("settings.py" 0 11 (:parent #179))) #("to match your path.\n" 0 20 (:parent #172)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #149))) :mode nil :granularity nil :parent #136) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #149) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #152) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #155)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #150))) :mode nil :granularity nil :parent #136) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #150) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #153) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #156))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #153) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #151))) :mode nil :granularity nil :parent #136) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #151) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #154) #("See " 0 4 (:parent #157)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #(".\n" 0 2 (:parent #157))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #152))) :mode nil :granularity nil :parent #136) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #152) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #155) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #158)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #158))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #153))) :mode nil :granularity nil :parent #136) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #156))) :mode section :granularity nil :parent #153) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #156) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #159) #("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 #162)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #162) #("PATH" 0 4 (:parent #166))) #("and R" 0 5 (:parent #162)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #162) #("LIBS" 0 4 (:parent #168))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #162) #("SITE" 0 4 (:parent #169))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #162))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #159)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #159) #("On one system:\n" 0 15 (:parent #164))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #159)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #159) #("and perhaps a few more.\n" 0 24 (:parent #166))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #157)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #157) #("data" 0 4 (:parent #199))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #157)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #157) #("files" 0 5 (:parent #201))) #("/genotype'" 0 10 (:parent #157))) :mode nil :granularity nil :parent #153) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #157) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #160) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #163)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #163) #("data" 0 4 (:parent #167))) #(". 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 #163)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #163) #("settings.py" 0 11 (:parent #169))) #("(see above in\nthis document).\n" 0 30 (:parent #163))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #160) #("You can use the GENENETWORK" 0 27 (:parent #164)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #164) #("FILES" 0 5 (:parent #168))) #("switch to set the datadir, for example\n" 0 39 (:parent #164))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #158))) :mode nil :granularity nil :parent #153) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #158) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #161) #("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 #164))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #159))) :mode nil :granularity nil :parent #153) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #159) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #162) #("This error\n" 0 11 (:parent #165))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #162)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #162) #("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 #167))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #162) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #168)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #168) #("LIBS" 0 4 (:parent #172))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #168) #("SITE" 0 4 (:parent #173))) #(". 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 #168))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #160))) :mode nil :granularity nil :parent #153) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #160) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #163) #("The following error\n" 0 20 (:parent #166))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #163)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #163) #("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 #168))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #163)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #163) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #170))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #163)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #163) #("if that works run genenetwork after setting SQL" 0 47 (:parent #172)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #172) #("URI" 0 3 (:parent #176))) #("to something like\n" 0 18 (:parent #172))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #163))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #154))) :mode nil :granularity nil :parent #136) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #157))) :mode section :granularity nil :parent #154) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #157) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #160) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #163))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #183) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #186)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #186)) #("\n" 0 1 (:parent #186)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #176) #("Create a gn2 user and home with space\n" 0 38 (:parent #179)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#177) #("Install redis\n" 0 14 (:parent #180))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #177) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #184) #("add to systemd\n" 0 15 (:parent #187)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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(13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #186) #("update database\n" 0 16 (:parent #189)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #148)) (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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #148) #("Guix-notes" 0 10 (:parent #154))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #148))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #145) #("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 #149)) (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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #149) #("Guix bioinformatics" 0 19 (:parent #153))) #("and " 0 4 (:parent #149)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #149) #("GNU Guix" 0 8 (:parent #155))) #(".\n" 0 2 (:parent #149))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #145) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #150)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #150) #("GN2 Dependency Graph" 0 20 (:parent #154))) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #143))) :mode nil :granularity nil :parent #137) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #143) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #146) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #149))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #150) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #158) #("Mariadb\n" 0 8 (:parent #161))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #144))) :mode nil :granularity nil :parent #137) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #144) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #147) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #150)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #150)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #150))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #145))) :mode nil :granularity nil :parent #137) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #145) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #148) #("We run a GNU Guix channel with packages at " 0 43 (:parent #151)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #151) #("guix-bioinformatics" 0 19 (:parent #155))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #151)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #151) #("PACKAGE" 0 7 (:parent #157))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #151) #("PATH" 0 4 (:parent #158))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #151))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #148) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #153))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #148) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #155))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #148) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #157))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #148) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #159)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #159) #("substitutes" 0 11 (:parent #163))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #159)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\"` switch.\n" 0 11 (:parent #159))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #148) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #160))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #148) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #162))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #146))) :mode nil :granularity nil :parent #137) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #146) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #149) #("Check out the source with git:\n" 0 31 (:parent #152))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #149) #("Run GN2 with above Guix profile\n" 0 32 (:parent #154))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #149) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #156))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #149) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #157))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #149) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #158))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #149) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #159))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #149) #("And browse on your local machine to " 0 36 (:parent #160)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n" 0 1 (:parent #160))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #147))) :mode nil :granularity nil :parent #137) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #147) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #150) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #153)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #153) #("README" 0 6 (:parent #157))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #153))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #148))) :mode nil :granularity nil :parent #137) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #148) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #151) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #154))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #149))) :mode nil :granularity nil :parent #137) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #152))) :mode section :granularity nil :parent #149) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #152) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #155) #("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 #158))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #155) #("As root configure the Guix profile\n" 0 35 (:parent #159))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #155)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #155) #("and run for example\n" 0 20 (:parent #161))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #155)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #155) #("If you want to run as root you may have to set\n" 0 47 (:parent #163))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #155) #("You also need to set\n" 0 21 (:parent #165))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #155) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #167))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #155) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #168))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #155) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #170))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #155) #("When you get errors like:\n" 0 26 (:parent #172))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #155) #("you may need to set\n" 0 20 (:parent #174))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #155)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #153))) :mode nil :granularity nil :parent #149) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #153) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #156) #("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 #159)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #159) #("webqtl" 0 6 (:parent #163))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #159) #("s" 0 1 (:parent #164))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #159)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #159) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #159) #("plant" 0 5 (:parent #167))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #159))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #156) #("Download one database from\n" 0 27 (:parent #160))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #156) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\n" 0 1 (:parent #161))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #156) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #162))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #156) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #164))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #156)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #156) #("and\n" 0 4 (:parent #167))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #156) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #169))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #156) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #171))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #156) #("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 #172))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #156) #("Note for the plant database you can rename it to db" 0 51 (:parent #173)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #173) #("webqtl" 0 6 (:parent #177))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #173) #("s" 0 1 (:parent #178))) #(", or\nchange the settings in etc/default" 0 39 (:parent #173)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #173) #("settings.py" 0 11 (:parent #180))) #("to match your path.\n" 0 20 (:parent #173)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #150))) :mode nil :granularity nil :parent #137) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #150) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #153) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #156)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #151))) :mode nil :granularity nil :parent #137) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #151) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #154) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #157))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #154) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n" 0 1 (:parent #158))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #152))) :mode nil :granularity nil :parent #137) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #152) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #155) #("See " 0 4 (:parent #158)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #(".\n" 0 2 (:parent #158))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #153))) :mode nil :granularity nil :parent #137) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #153) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #156) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #159)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #159))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #154))) :mode nil :granularity nil :parent #137) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #157))) :mode section :granularity nil :parent #154) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #157) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #160) #("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 #163)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #163) #("PATH" 0 4 (:parent #167))) #("and R" 0 5 (:parent #163)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #163) #("LIBS" 0 4 (:parent #169))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #163) #("SITE" 0 4 (:parent #170))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #163))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #160)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #160) #("On one system:\n" 0 15 (:parent #165))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #160)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #160) #("and perhaps a few more.\n" 0 24 (:parent #167))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #158)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #158) #("data" 0 4 (:parent #200))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #158)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #158) #("files" 0 5 (:parent #202))) #("/genotype'" 0 10 (:parent #158))) :mode nil :granularity nil :parent #154) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #158) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #161) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #164)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #164) #("data" 0 4 (:parent #168))) #(". 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 #164)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #164) #("settings.py" 0 11 (:parent #170))) #("(see above in\nthis document).\n" 0 30 (:parent #164))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #161) #("You can use the GENENETWORK" 0 27 (:parent #165)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #165) #("FILES" 0 5 (:parent #169))) #("switch to set the datadir, for example\n" 0 39 (:parent #165))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #161)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #159))) :mode nil :granularity nil :parent #154) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #159) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #162) #("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 #165))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #160))) :mode nil :granularity nil :parent #154) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #160) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #163) #("This error\n" 0 11 (:parent #166))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #163)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #163) #("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 #168))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #163) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #169)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #169) #("LIBS" 0 4 (:parent #173))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #169) #("SITE" 0 4 (:parent #174))) #(". 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 #169))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #161))) :mode nil :granularity nil :parent #154) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #161) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #164) #("The following error\n" 0 20 (:parent #167))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #164)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #164) #("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 #169))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #164)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #164) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #171))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #164)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #164) #("if that works run genenetwork after setting SQL" 0 47 (:parent #173)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #173) #("URI" 0 3 (:parent #177))) #("to something like\n" 0 18 (:parent #173))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #164))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #155))) :mode nil :granularity nil :parent #137) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #158))) :mode section :granularity nil :parent #155) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #158) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #161) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #164))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #184) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #187)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #187)) #("\n" 0 1 (:parent #187)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #177) #("Create a gn2 user and home with space\n" 0 38 (:parent #180)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#178) #("Install redis\n" 0 14 (:parent #181))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #178) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #185) #("add to systemd\n" 0 15 (:parent #188)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #182) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #186) #("update redis.cnf\n" 0 17 (:parent #189)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #182) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #187) #("update database\n" 0 16 (:parent #190)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #149)) (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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #149) #("Guix-notes" 0 10 (:parent #155))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #149))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #146) #("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 #150)) (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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #150) #("Guix bioinformatics" 0 19 (:parent #154))) #("and " 0 4 (:parent #150)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #150) #("GNU Guix" 0 8 (:parent #156))) #(".\n" 0 2 (:parent #150))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #146) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #151)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #151) #("GN2 Dependency Graph" 0 20 (:parent #155))) #(".\n" 0 2 (:parent #151))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #144))) :mode nil :granularity nil :parent #138) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #144) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #147) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #150))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #151) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #159) #("Mariadb\n" 0 8 (:parent #162))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #145))) :mode nil :granularity nil :parent #138) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #145) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #148) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #151)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #151)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #151))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #146))) :mode nil :granularity nil :parent #138) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #146) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #149) #("We run a GNU Guix channel with packages at " 0 43 (:parent #152)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #152) #("guix-bioinformatics" 0 19 (:parent #156))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #152)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #152) #("PACKAGE" 0 7 (:parent #158))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #152) #("PATH" 0 4 (:parent #159))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #152))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #149) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #154))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #149) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #156))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #149) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #158))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #149) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #160)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #160) #("substitutes" 0 11 (:parent #164))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #160)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #160)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #160)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\"` switch.\n" 0 11 (:parent #160))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #149) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #161))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #149) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #163))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #147))) :mode nil :granularity nil :parent #138) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #147) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #150) #("Check out the source with git:\n" 0 31 (:parent #153))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #150) #("Run GN2 with above Guix profile\n" 0 32 (:parent #155))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #150) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #157))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #150) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #158))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #150) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #159))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #150) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #160))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #150) #("And browse on your local machine to " 0 36 (:parent #161)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\n" 0 1 (:parent #161))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #148))) :mode nil :granularity nil :parent #138) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #148) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #151) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #154)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #154) #("README" 0 6 (:parent #158))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #154))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #149))) :mode nil :granularity nil :parent #138) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #149) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #152) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #155))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #150))) :mode nil :granularity nil :parent #138) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #153))) :mode section :granularity nil :parent #150) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #153) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #156) #("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 #159))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #156) #("As root configure the Guix profile\n" 0 35 (:parent #160))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #156)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #156) #("and run for example\n" 0 20 (:parent #162))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #156)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #156) #("If you want to run as root you may have to set\n" 0 47 (:parent #164))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #156) #("You also need to set\n" 0 21 (:parent #166))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #156) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #168))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #156) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #169))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #156) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #171))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #156) #("When you get errors like:\n" 0 26 (:parent #173))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #156) #("you may need to set\n" 0 20 (:parent #175))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #154))) :mode nil :granularity nil :parent #150) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #154) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #157) #("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 #160)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #160) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #160) #("s" 0 1 (:parent #165))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #160)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #160) #("webqtl" 0 6 (:parent #167))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #160) #("plant" 0 5 (:parent #168))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #160))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #157) #("Download one database from\n" 0 27 (:parent #161))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #157) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n" 0 1 (:parent #162))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #157) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #163))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #157) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #165))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #157)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #157) #("and\n" 0 4 (:parent #168))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #157) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #170))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #157) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #172))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #157) #("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 #173))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #157) #("Note for the plant database you can rename it to db" 0 51 (:parent #174)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #174) #("webqtl" 0 6 (:parent #178))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #174) #("s" 0 1 (:parent #179))) #(", or\nchange the settings in etc/default" 0 39 (:parent #174)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #174) #("settings.py" 0 11 (:parent #181))) #("to match your path.\n" 0 20 (:parent #174)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #151))) :mode nil :granularity nil :parent #138) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #151) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #154) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #157)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #152))) :mode nil :granularity nil :parent #138) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #152) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #155) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #158))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #155) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n" 0 1 (:parent #159))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #153))) :mode nil :granularity nil :parent #138) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #153) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #156) #("See " 0 4 (:parent #159)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #154))) :mode nil :granularity nil :parent #138) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #154) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #157) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #160)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #160))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #155))) :mode nil :granularity nil :parent #138) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #158))) :mode section :granularity nil :parent #155) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #158) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #161) #("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 #164)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #164) #("PATH" 0 4 (:parent #168))) #("and R" 0 5 (:parent #164)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #164) #("LIBS" 0 4 (:parent #170))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #164) #("SITE" 0 4 (:parent #171))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #164))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #161)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #161) #("On one system:\n" 0 15 (:parent #166))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #161)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #161) #("and perhaps a few more.\n" 0 24 (:parent #168))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #159)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #159) #("data" 0 4 (:parent #201))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #159)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #159) #("files" 0 5 (:parent #203))) #("/genotype'" 0 10 (:parent #159))) :mode nil :granularity nil :parent #155) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #159) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #162) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #165)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #165) #("data" 0 4 (:parent #169))) #(". 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 #165)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #165) #("settings.py" 0 11 (:parent #171))) #("(see above in\nthis document).\n" 0 30 (:parent #165))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #162) #("You can use the GENENETWORK" 0 27 (:parent #166)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #166) #("FILES" 0 5 (:parent #170))) #("switch to set the datadir, for example\n" 0 39 (:parent #166))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #162)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #160))) :mode nil :granularity nil :parent #155) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #160) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #163) #("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 #166))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #161))) :mode nil :granularity nil :parent #155) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #161) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #164) #("This error\n" 0 11 (:parent #167))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #164)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #164) #("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 #169))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #164) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #170)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #170) #("LIBS" 0 4 (:parent #174))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #170) #("SITE" 0 4 (:parent #175))) #(". 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 #170))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #162))) :mode nil :granularity nil :parent #155) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #162) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #165) #("The following error\n" 0 20 (:parent #168))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #165)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #165) #("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 #170))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #165)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #165) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #172))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #165)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #165) #("if that works run genenetwork after setting SQL" 0 47 (:parent #174)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #174) #("URI" 0 3 (:parent #178))) #("to something like\n" 0 18 (:parent #174))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #165))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #156))) :mode nil :granularity nil :parent #138) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #159))) :mode section :granularity nil :parent #156) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #159) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #162) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #165))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #185) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #188)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #("\n" 0 1 (:parent #188)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #173) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #178) #("Create a gn2 user and home with space\n" 0 38 (:parent #181)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#179) #("Install redis\n" 0 14 (:parent #182))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #179) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #186) #("add to systemd\n" 0 15 (:parent #189)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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(13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #183) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #188) #("update database\n" 0 16 (:parent #191)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #150)) (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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #150) #("Guix-notes" 0 10 (:parent #156))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #150))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #147) #("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 #151)) (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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #151) #("Guix bioinformatics" 0 19 (:parent #155))) #("and " 0 4 (:parent #151)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #151) #("GNU Guix" 0 8 (:parent #157))) #(".\n" 0 2 (:parent #151))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #147) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #152)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #152) #("GN2 Dependency Graph" 0 20 (:parent #156))) #(".\n" 0 2 (:parent #152))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #145))) :mode nil :granularity nil :parent #139) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #145) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #148) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #151))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #152) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #160) #("Mariadb\n" 0 8 (:parent #163))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #146))) :mode nil :granularity nil :parent #139) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #146) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #149) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #152)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #152)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #152))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #147))) :mode nil :granularity nil :parent #139) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #147) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #150) #("We run a GNU Guix channel with packages at " 0 43 (:parent #153)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #153) #("guix-bioinformatics" 0 19 (:parent #157))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #153)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #153) #("PACKAGE" 0 7 (:parent #159))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #153) #("PATH" 0 4 (:parent #160))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #153))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #150) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #155))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #150) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #157))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #150) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #159))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #150) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #161)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #161) #("substitutes" 0 11 (:parent #165))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #161)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #161)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #161)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\"` switch.\n" 0 11 (:parent #161))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #150) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #162))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #150) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #164))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #148))) :mode nil :granularity nil :parent #139) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #148) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #151) #("Check out the source with git:\n" 0 31 (:parent #154))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #151) #("Run GN2 with above Guix profile\n" 0 32 (:parent #156))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #151) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #158))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #151) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #159))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #151) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #160))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #151) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #161))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #151) #("And browse on your local machine to " 0 36 (:parent #162)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\n" 0 1 (:parent #162))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #149))) :mode nil :granularity nil :parent #139) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #149) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #152) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #155)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #155) #("README" 0 6 (:parent #159))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #155))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #150))) :mode nil :granularity nil :parent #139) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #150) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #153) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #156))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #151))) :mode nil :granularity nil :parent #139) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #154))) :mode section :granularity nil :parent #151) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #154) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #157) #("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 #160))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #157) #("As root configure the Guix profile\n" 0 35 (:parent #161))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #157)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #157) #("and run for example\n" 0 20 (:parent #163))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #157)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #157) #("If you want to run as root you may have to set\n" 0 47 (:parent #165))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #157) #("You also need to set\n" 0 21 (:parent #167))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #157) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #169))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #157) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #170))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #157) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #172))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #157) #("When you get errors like:\n" 0 26 (:parent #174))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #157) #("you may need to set\n" 0 20 (:parent #176))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #157)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #155))) :mode nil :granularity nil :parent #151) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #155) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #158) #("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 #161)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #161) #("webqtl" 0 6 (:parent #165))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #161) #("s" 0 1 (:parent #166))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #161)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #161) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #161) #("plant" 0 5 (:parent #169))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #161))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #158) #("Download one database from\n" 0 27 (:parent #162))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #158) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\n" 0 1 (:parent #163))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #158) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #164))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #158) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #166))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #158)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #158) #("and\n" 0 4 (:parent #169))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #158) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #171))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #158) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #173))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #158) #("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 #174))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #158) #("Note for the plant database you can rename it to db" 0 51 (:parent #175)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #175) #("webqtl" 0 6 (:parent #179))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #175) #("s" 0 1 (:parent #180))) #(", or\nchange the settings in etc/default" 0 39 (:parent #175)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #175) #("settings.py" 0 11 (:parent #182))) #("to match your path.\n" 0 20 (:parent #175)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #152))) :mode nil :granularity nil :parent #139) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #152) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #155) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #158)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n" 0 1 (:parent #158))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #155)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #153))) :mode nil :granularity nil :parent #139) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #153) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #156) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #159))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #156) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n" 0 1 (:parent #160))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #154))) :mode nil :granularity nil :parent #139) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #154) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #157) #("See " 0 4 (:parent #160)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #155))) :mode nil :granularity nil :parent #139) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #155) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #158) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #161)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #161))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #156))) :mode nil :granularity nil :parent #139) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #159))) :mode section :granularity nil :parent #156) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #159) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #162) #("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 #165)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #165) #("PATH" 0 4 (:parent #169))) #("and R" 0 5 (:parent #165)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #165) #("LIBS" 0 4 (:parent #171))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #165) #("SITE" 0 4 (:parent #172))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #165))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #162)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #162) #("On one system:\n" 0 15 (:parent #167))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #162)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #162) #("and perhaps a few more.\n" 0 24 (:parent #169))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #160)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #160) #("data" 0 4 (:parent #202))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #160)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #160) #("files" 0 5 (:parent #204))) #("/genotype'" 0 10 (:parent #160))) :mode nil :granularity nil :parent #156) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #160) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #163) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #166)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #166) #("data" 0 4 (:parent #170))) #(". 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 #166)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #166) #("settings.py" 0 11 (:parent #172))) #("(see above in\nthis document).\n" 0 30 (:parent #166))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #163) #("You can use the GENENETWORK" 0 27 (:parent #167)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #167) #("FILES" 0 5 (:parent #171))) #("switch to set the datadir, for example\n" 0 39 (:parent #167))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #163)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #161))) :mode nil :granularity nil :parent #156) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #161) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #164) #("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 #167))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #162))) :mode nil :granularity nil :parent #156) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #162) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #165) #("This error\n" 0 11 (:parent #168))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #165)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #165) #("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 #170))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #165) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #171)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #171) #("LIBS" 0 4 (:parent #175))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #171) #("SITE" 0 4 (:parent #176))) #(". 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 #171))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #163))) :mode nil :granularity nil :parent #156) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #163) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #166) #("The following error\n" 0 20 (:parent #169))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #166)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #166) #("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 #171))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #166)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #166) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #173))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #166)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #166) #("if that works run genenetwork after setting SQL" 0 47 (:parent #175)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #175) #("URI" 0 3 (:parent #179))) #("to something like\n" 0 18 (:parent #175))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #166))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #157))) :mode nil :granularity nil :parent #139) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #160))) :mode section :granularity nil :parent #157) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #160) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #163) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #166))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #186) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #189)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #174) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #179) #("Create a gn2 user and home with space\n" 0 38 (:parent #182)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#180) #("Install redis\n" 0 14 (:parent #183))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #180) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #187) #("add to systemd\n" 0 15 (:parent #190)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #184) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #188) #("update redis.cnf\n" 0 17 (:parent #191)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #184) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #189) #("update database\n" 0 16 (:parent #192)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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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 #151)) (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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #151) #("Guix-notes" 0 10 (:parent #157))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #151))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #148) #("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 #152)) (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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #152) #("Guix bioinformatics" 0 19 (:parent #156))) #("and " 0 4 (:parent #152)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #152) #("GNU Guix" 0 8 (:parent #158))) #(".\n" 0 2 (:parent #152))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #148) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #153)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #153) #("GN2 Dependency Graph" 0 20 (:parent #157))) #(".\n" 0 2 (:parent #153))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #146))) :mode nil :granularity nil :parent #140) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #146) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #149) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #152))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #149) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #156) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #159)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #157) #("A path to the (static) genotype files\n" 0 38 (:parent #160)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #158) #("Gn-proxy for authentication\n" 0 28 (:parent #161)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #159) #("The genenetwork3 service\n" 0 25 (:parent #162)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #160) #("Redis\n" 0 6 (:parent #163)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #153) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #161) #("Mariadb\n" 0 8 (:parent #164))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #147))) :mode nil :granularity nil :parent #140) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #147) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #150) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #153)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #153)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #153))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #148))) :mode nil :granularity nil :parent #140) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #148) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #151) #("We run a GNU Guix channel with packages at " 0 43 (:parent #154)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #154) #("guix-bioinformatics" 0 19 (:parent #158))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #154)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #154) #("PACKAGE" 0 7 (:parent #160))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #154) #("PATH" 0 4 (:parent #161))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #154))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #151)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #151) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #156))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #151)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #151) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #158))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #151)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #151) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #160))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #151) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #162)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #162) #("substitutes" 0 11 (:parent #166))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #162)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #162)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #162)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #("\"` switch.\n" 0 11 (:parent #162))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #151) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #163))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #151) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #165))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #149))) :mode nil :granularity nil :parent #140) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #149) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #152) #("Check out the source with git:\n" 0 31 (:parent #155))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #152) #("Run GN2 with above Guix profile\n" 0 32 (:parent #157))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #152) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #159))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #152) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #160))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #152) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #161))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #152) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #162))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #152) #("And browse on your local machine to " 0 36 (:parent #163)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\n" 0 1 (:parent #163))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #150))) :mode nil :granularity nil :parent #140) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #150) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #153) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #156)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #156) #("README" 0 6 (:parent #160))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #156))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #151))) :mode nil :granularity nil :parent #140) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #151) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #154) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #157))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #152))) :mode nil :granularity nil :parent #140) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #155) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #158) #("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 #161))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #158) #("As root configure the Guix profile\n" 0 35 (:parent #162))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #158)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #158) #("and run for example\n" 0 20 (:parent #164))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #158)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #158) #("If you want to run as root you may have to set\n" 0 47 (:parent #166))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #158) #("You also need to set\n" 0 21 (:parent #168))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #158) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #170))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #158) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #171))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #158) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #173))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #158) #("When you get errors like:\n" 0 26 (:parent #175))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #158) #("you may need to set\n" 0 20 (:parent #177))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #158)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #156))) :mode nil :granularity nil :parent #152) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #156) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #159) #("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 #162)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #162) #("s" 0 1 (:parent #167))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #162)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #169))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #162) #("plant" 0 5 (:parent #170))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #162))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #159) #("Download one database from\n" 0 27 (:parent #163))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #159) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #164)) #("\n" 0 1 (:parent #164))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #159) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #165))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #159) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #167))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #159)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #159) #("and\n" 0 4 (:parent #170))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #159) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #172))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #159) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #174))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #159) #("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 #175))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #159) #("Note for the plant database you can rename it to db" 0 51 (:parent #176)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #176) #("webqtl" 0 6 (:parent #180))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #176) #("s" 0 1 (:parent #181))) #(", or\nchange the settings in etc/default" 0 39 (:parent #176)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #176) #("settings.py" 0 11 (:parent #183))) #("to match your path.\n" 0 20 (:parent #176)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #153))) :mode nil :granularity nil :parent #140) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #153) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #156) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #159)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n" 0 1 (:parent #159))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #154))) :mode nil :granularity nil :parent #140) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #154) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #157) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #160))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #157) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #("\n" 0 1 (:parent #161))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #155))) :mode nil :granularity nil :parent #140) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #155) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #158) #("See " 0 4 (:parent #161)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #161)) #(".\n" 0 2 (:parent #161))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #156))) :mode nil :granularity nil :parent #140) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #156) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #159) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #162)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #162)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #162))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #157))) :mode nil :granularity nil :parent #140) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #160))) :mode section :granularity nil :parent #157) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #160) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #163) #("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 #166)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #166) #("PATH" 0 4 (:parent #170))) #("and R" 0 5 (:parent #166)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #166) #("LIBS" 0 4 (:parent #172))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #166) #("SITE" 0 4 (:parent #173))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #166))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #163)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #163) #("On one system:\n" 0 15 (:parent #168))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #163)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #163) #("and perhaps a few more.\n" 0 24 (:parent #170))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #161)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #161) #("data" 0 4 (:parent #203))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #161)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #161) #("files" 0 5 (:parent #205))) #("/genotype'" 0 10 (:parent #161))) :mode nil :granularity nil :parent #157) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #161) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #164) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #167)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #167) #("data" 0 4 (:parent #171))) #(". 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 #167)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #167) #("settings.py" 0 11 (:parent #173))) #("(see above in\nthis document).\n" 0 30 (:parent #167))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #164) #("You can use the GENENETWORK" 0 27 (:parent #168)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #168) #("FILES" 0 5 (:parent #172))) #("switch to set the datadir, for example\n" 0 39 (:parent #168))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #164)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #162))) :mode nil :granularity nil :parent #157) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #162) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #165) #("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 #168))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #163))) :mode nil :granularity nil :parent #157) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #163) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #166) #("This error\n" 0 11 (:parent #169))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #166)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #166) #("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 #171))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #166) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #172)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #172) #("LIBS" 0 4 (:parent #176))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #172) #("SITE" 0 4 (:parent #177))) #(". 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 #172))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #164))) :mode nil :granularity nil :parent #157) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #164) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #167) #("The following error\n" 0 20 (:parent #170))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #167)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #167) #("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 #172))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #167)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #167) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #174))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #167)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #167) #("if that works run genenetwork after setting SQL" 0 47 (:parent #176)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #176) #("URI" 0 3 (:parent #180))) #("to something like\n" 0 18 (:parent #176))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #167))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #158))) :mode nil :granularity nil :parent #140) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #161))) :mode section :granularity nil :parent #158) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #161) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #164) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #167))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #164) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #168) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #171) #("Base install\n" 0 13 (:parent #174))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #171) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #175) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #178) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #181)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #175) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #179) #("Get Guix build going\n" 0 21 (:parent #182))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #179) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #183) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #186) #("Build the correct version of Guix\n" 0 34 (:parent #189)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #183) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #187) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #190)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #("\n" 0 1 (:parent #190)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #183) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #188) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #191)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #175) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #180) #("Create a gn2 user and home with space\n" 0 38 (:parent #183)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #175) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #181) #("Install redis\n" 0 14 (:parent #184))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #181) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #188) #("add to systemd\n" 0 15 (:parent #191)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #189) #("update redis.cnf\n" 0 17 (:parent #192)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #190) #("update database\n" 0 16 (:parent #193)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #112) #("Gn-proxy for authentication\n" 0 28 (:parent #115)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #113) #("The genenetwork3 service\n" 0 25 (:parent #116)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #114) #("Redis\n" 0 6 (:parent #117)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #115) #("Mariadb\n" 0 8 (:parent #118))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #101) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #104) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #107)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #107)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #107))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #104)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #102))) :mode nil :granularity nil :parent #94) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #102) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #105) #("We run a GNU Guix channel with packages at " 0 43 (:parent #108)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #108) #("guix-bioinformatics" 0 19 (:parent #112))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #108)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #108) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #108) #("PATH" 0 4 (:parent #115))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #108))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #105) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #110))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #105) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #112))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #105) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #114))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #105)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #105) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #116)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #116) #("substitutes" 0 11 (:parent #120))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #116)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #116)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #116)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\"` switch.\n" 0 11 (:parent #116))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #105) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #117))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #105)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #105) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #119))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #103) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #106) #("Check out the source with git:\n" 0 31 (:parent #109))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #106)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #106) #("Run GN2 with above Guix profile\n" 0 32 (:parent #111))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #106)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #106) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #113))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #106) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #114))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #106) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #115))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #106) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #116))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #106) #("And browse on your local machine to " 0 36 (:parent #117)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #117)) #("\n" 0 1 (:parent #117))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #104))) :mode nil :granularity nil :parent #94) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #104) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #107) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #110)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #110) #("README" 0 6 (:parent #114))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #110))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #105) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #108) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #111))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #106))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #109))) :mode section :granularity nil :parent #106) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #109) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #112) #("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 #115))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #112) #("As root configure the Guix profile\n" 0 35 (:parent #116))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #112) #("and run for example\n" 0 20 (:parent #118))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #112) #("If you want to run as root you may have to set\n" 0 47 (:parent #120))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #112) #("You also need to set\n" 0 21 (:parent #122))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #112) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #124))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #112) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #125))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #112) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #127))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #112) #("When you get errors like:\n" 0 26 (:parent #129))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #112) #("you may need to set\n" 0 20 (:parent #131))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #112)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #110))) :mode nil :granularity nil :parent #106) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #110) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #113) #("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 #116)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #116) #("webqtl" 0 6 (:parent #120))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #116) #("s" 0 1 (:parent #121))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #116)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #116) #("webqtl" 0 6 (:parent #123))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #116) #("plant" 0 5 (:parent #124))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #116))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #113) #("Download one database from\n" 0 27 (:parent #117))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #113) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #118)) #("\n" 0 1 (:parent #118))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #113) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #119))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #113) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #121))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #113)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #113) #("and\n" 0 4 (:parent #124))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #113) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #126))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #113) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #128))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #113) #("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 #129))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #113) #("Note for the plant database you can rename it to db" 0 51 (:parent #130)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #130) #("webqtl" 0 6 (:parent #134))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #130) #("s" 0 1 (:parent #135))) #(", or\nchange the settings in etc/default" 0 39 (:parent #130)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #130) #("settings.py" 0 11 (:parent #137))) #("to match your path.\n" 0 20 (:parent #130)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #107) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #110) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #113)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #("\n" 0 1 (:parent #113))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #110)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #108))) :mode nil :granularity nil :parent #94) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #108) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #111) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #114))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #111) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #("\n" 0 1 (:parent #115))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #109))) :mode nil :granularity nil :parent #94) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #109) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #112) #("See " 0 4 (:parent #115)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #(".\n" 0 2 (:parent #115))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #110))) :mode nil :granularity nil :parent #94) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #110) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #113) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #116)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #116))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #111))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #114))) :mode section :granularity nil :parent #111) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #114) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #117) #("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 #120)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #120) #("PATH" 0 4 (:parent #124))) #("and R" 0 5 (:parent #120)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #120) #("LIBS" 0 4 (:parent #126))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #120) #("SITE" 0 4 (:parent #127))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #120))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #117)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #117) #("On one system:\n" 0 15 (:parent #122))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #117)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #117) #("and perhaps a few more.\n" 0 24 (:parent #124))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #115)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #115) #("data" 0 4 (:parent #157))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #115)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #115) #("files" 0 5 (:parent #159))) #("/genotype'" 0 10 (:parent #115))) :mode nil :granularity nil :parent #111) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #115) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #118) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #121)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #121) #("data" 0 4 (:parent #125))) #(". 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 #121)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #121) #("settings.py" 0 11 (:parent #127))) #("(see above in\nthis document).\n" 0 30 (:parent #121))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #118) #("You can use the GENENETWORK" 0 27 (:parent #122)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #122) #("FILES" 0 5 (:parent #126))) #("switch to set the datadir, for example\n" 0 39 (:parent #122))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #118)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #116))) :mode nil :granularity nil :parent #111) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #116) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #119) #("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 #122))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #117))) :mode nil :granularity nil :parent #111) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #117) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #120) #("This error\n" 0 11 (:parent #123))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #120)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #120) #("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 #125))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #120) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #126)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #126) #("LIBS" 0 4 (:parent #130))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #126) #("SITE" 0 4 (:parent #131))) #(". 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 #126))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #118))) :mode nil :granularity nil :parent #111) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #118) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #121) #("The following error\n" 0 20 (:parent #124))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #121)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #121) #("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 #126))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #121)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #121) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #128))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #121)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #121) #("if that works run genenetwork after setting SQL" 0 47 (:parent #130)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #130) #("URI" 0 3 (:parent #134))) #("to something like\n" 0 18 (:parent #130))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #121))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #112))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #115))) :mode section :granularity nil :parent #112) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #115) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #118) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #121))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #141) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #144)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #("\n" 0 1 (:parent #144)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #129) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #134) #("Create a gn2 user and home with space\n" 0 38 (:parent #137)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#135) #("Install redis\n" 0 14 (:parent #138))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #135) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #142) #("add to systemd\n" 0 15 (:parent #145)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #143) #("update redis.cnf\n" 0 17 (:parent #146)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #139) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #144) #("update database\n" 0 16 (:parent #147)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #343) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #347) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #354) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #357)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #362) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #366) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #369) #("Base install\n" 0 13 (:parent #372))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #369) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #376) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #379)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #377) #("Get Guix build going\n" 0 21 (:parent #380))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #377) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #384) #("Build the correct version of Guix\n" 0 34 (:parent #387)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #99) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #102) #("Large system deployments can get very " 0 38 (:parent #105)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket 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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 #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #111))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #106) #("GNU Guix" 0 8 (:parent #112))) #(".\n" 0 2 (:parent #106))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #102) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #107)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #107) #("GN2 Dependency Graph" 0 20 (:parent #111))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #100))) :mode nil :granularity nil :parent #94) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #100) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #103) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #106))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #111) #("A path to the (static) genotype files\n" 0 38 (:parent #114)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #112) #("Gn-proxy for authentication\n" 0 28 (:parent #115)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #113) #("The genenetwork3 service\n" 0 25 (:parent #116)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #114) #("Redis\n" 0 6 (:parent #117)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #107) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #115) #("Mariadb\n" 0 8 (:parent #118))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #101) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #104) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #107)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #107)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #107))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #104)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #102))) :mode nil :granularity nil :parent #94) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #102) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #105) #("We run a GNU Guix channel with packages at " 0 43 (:parent #108)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #108) #("guix-bioinformatics" 0 19 (:parent #112))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #108)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #108) #("PACKAGE" 0 7 (:parent #114))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #108) #("PATH" 0 4 (:parent #115))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #108))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #105) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #110))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #105) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #112))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #105)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #105) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #114))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #105)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #105) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #116)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #116) #("substitutes" 0 11 (:parent #120))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #116)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #116)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #116)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\"` switch.\n" 0 11 (:parent #116))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #105) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #117))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #105)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #105) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #119))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #103) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #106) #("Check out the source with git:\n" 0 31 (:parent #109))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #106)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #106) #("Run GN2 with above Guix profile\n" 0 32 (:parent #111))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #106)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #106) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #113))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #106) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #114))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #106) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #115))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #106) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #116))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #106) #("And browse on your local machine to " 0 36 (:parent #117)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #117)) #("\n" 0 1 (:parent #117))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #104))) :mode nil :granularity nil :parent #94) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #104) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #107) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #110)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #110) #("README" 0 6 (:parent #114))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #110))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #105) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #108) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #111))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #106))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #109))) :mode section :granularity nil :parent #106) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #109) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #112) #("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 #115))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #112) #("As root configure the Guix profile\n" 0 35 (:parent #116))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #112) #("and run for example\n" 0 20 (:parent #118))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #112)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #112) #("If you want to run as root you may have to set\n" 0 47 (:parent #120))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #112) #("You also need to set\n" 0 21 (:parent #122))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #112) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #124))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #112) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #125))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #112) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #127))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #112) #("When you get errors like:\n" 0 26 (:parent #129))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #112)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #112) #("you may need to set\n" 0 20 (:parent #131))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #112)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #110))) :mode nil :granularity nil :parent #106) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #110) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #113) #("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 #116)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #116) #("webqtl" 0 6 (:parent #120))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #116) #("s" 0 1 (:parent #121))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #116)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #116) #("webqtl" 0 6 (:parent #123))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #116) #("plant" 0 5 (:parent #124))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #116))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #113) #("Download one database from\n" 0 27 (:parent #117))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #113) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #118)) #("\n" 0 1 (:parent #118))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #113) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #119))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #113) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #121))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #113)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #113) #("and\n" 0 4 (:parent #124))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #113) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #126))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #113)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #113) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #128))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #113) #("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 #129))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #113) #("Note for the plant database you can rename it to db" 0 51 (:parent #130)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #130) #("webqtl" 0 6 (:parent #134))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #130) #("s" 0 1 (:parent #135))) #(", or\nchange the settings in etc/default" 0 39 (:parent #130)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #130) #("settings.py" 0 11 (:parent #137))) #("to match your path.\n" 0 20 (:parent #130)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #107) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #110) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #113)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #("\n" 0 1 (:parent #113))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #110)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #108))) :mode nil :granularity nil :parent #94) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #108) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #111) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #114))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #111) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #("\n" 0 1 (:parent #115))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #109))) :mode nil :granularity nil :parent #94) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #109) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #112) #("See " 0 4 (:parent #115)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #(".\n" 0 2 (:parent #115))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #110))) :mode nil :granularity nil :parent #94) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #110) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #113) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #116)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #116))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #111))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #114))) :mode section :granularity nil :parent #111) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #114) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #117) #("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 #120)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #120) #("PATH" 0 4 (:parent #124))) #("and R" 0 5 (:parent #120)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #120) #("LIBS" 0 4 (:parent #126))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #120) #("SITE" 0 4 (:parent #127))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #120))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #117)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #117) #("On one system:\n" 0 15 (:parent #122))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #117)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #117) #("and perhaps a few more.\n" 0 24 (:parent #124))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #115)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #115) #("data" 0 4 (:parent #157))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #115)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #115) #("files" 0 5 (:parent #159))) #("/genotype'" 0 10 (:parent #115))) :mode nil :granularity nil :parent #111) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #115) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #118) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #121)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #121) #("data" 0 4 (:parent #125))) #(". 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 #121)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #121) #("settings.py" 0 11 (:parent #127))) #("(see above in\nthis document).\n" 0 30 (:parent #121))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #118) #("You can use the GENENETWORK" 0 27 (:parent #122)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #122) #("FILES" 0 5 (:parent #126))) #("switch to set the datadir, for example\n" 0 39 (:parent #122))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #118)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #116))) :mode nil :granularity nil :parent #111) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #116) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #119) #("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 #122))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #117))) :mode nil :granularity nil :parent #111) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #117) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #120) #("This error\n" 0 11 (:parent #123))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #120)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #120) #("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 #125))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #120) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #126)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #126) #("LIBS" 0 4 (:parent #130))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #126) #("SITE" 0 4 (:parent #131))) #(". 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 #126))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #118))) :mode nil :granularity nil :parent #111) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #118) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #121) #("The following error\n" 0 20 (:parent #124))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #121)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #121) #("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 #126))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #121)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #121) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #128))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #121)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #121) #("if that works run genenetwork after setting SQL" 0 47 (:parent #130)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #130) #("URI" 0 3 (:parent #134))) #("to something like\n" 0 18 (:parent #130))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #121))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #112))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #115))) :mode section :granularity nil :parent #112) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #115) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #118) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #121))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #118) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #122) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #125) #("Base install\n" 0 13 (:parent #128))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #125) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #129) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #132) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #135)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #129) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #133) #("Get Guix build going\n" 0 21 (:parent #136))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #133) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #137) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #140) #("Build the correct version of Guix\n" 0 34 (:parent #143)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #137) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #141) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #144)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #("\n" 0 1 (:parent #144)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #137) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #142) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #145)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #129) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #134) #("Create a gn2 user and home with space\n" 0 38 (:parent #137)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #129) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #135) #("Install redis\n" 0 14 (:parent #138))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #135) (item (:bullet "- " :begin 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:post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #98))) #49 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #100))) :mode nil :granularity nil :parent #95) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #100) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #103) #("Large system deployments can get very " 0 38 (:parent #106)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link 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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 #106)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #106) #("Guix-notes" 0 10 (:parent #112))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #106))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #103) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #107) #("Guix bioinformatics" 0 19 (:parent #111))) #("and " 0 4 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #107) #("GNU Guix" 0 8 (:parent #113))) #(".\n" 0 2 (:parent #107))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #103) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #108)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #108) #("GN2 Dependency Graph" 0 20 (:parent #112))) #(".\n" 0 2 (:parent #108))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #101))) :mode nil :granularity nil :parent #95) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #101) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #104) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #107))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #108) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #115) #("Redis\n" 0 6 (:parent #118)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. 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Follow the instructions on\n" 0 117 (:parent #108)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #108)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #108))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #105)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #103))) :mode nil :granularity nil :parent #95) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #103) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #106) #("We run a GNU Guix channel with packages at " 0 43 (:parent #109)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #109) #("guix-bioinformatics" 0 19 (:parent #113))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #109)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #109) #("PACKAGE" 0 7 (:parent #115))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #109) #("PATH" 0 4 (:parent #116))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #109))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #106)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #106) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #111))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #106)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #106) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #113))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #106)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #106) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #115))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #106)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #106) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #117)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #117) #("substitutes" 0 11 (:parent #121))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #117)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #117)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #117)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #117)) #("\"` switch.\n" 0 11 (:parent #117))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #106) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #118))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #106)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #106) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #120))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #104))) :mode nil :granularity nil :parent #95) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #104) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #107) #("Check out the source with git:\n" 0 31 (:parent #110))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #107)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #107) #("Run GN2 with above Guix profile\n" 0 32 (:parent #112))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #107)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #107) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #114))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #107) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #115))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #107) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #116))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #107) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #117))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #107) #("And browse on your local machine to " 0 36 (:parent #118)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #118)) #("\n" 0 1 (:parent #118))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #105))) :mode nil :granularity nil :parent #95) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #105) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #108) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #111)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #111) #("README" 0 6 (:parent #115))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #111))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #106))) :mode nil :granularity nil :parent #95) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #106) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #109) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #112))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #107))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #110))) :mode section :granularity nil :parent #107) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #110) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #113) #("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 #116))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #113) #("As root configure the Guix profile\n" 0 35 (:parent #117))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #113)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #113) #("and run for example\n" 0 20 (:parent #119))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #113)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #113) #("If you want to run as root you may have to set\n" 0 47 (:parent #121))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #113)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #113) #("You also need to set\n" 0 21 (:parent #123))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #113)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #113) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #125))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #113) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #126))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #113)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #113) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #128))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #113)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #113) #("When you get errors like:\n" 0 26 (:parent #130))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #113)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #113) #("you may need to set\n" 0 20 (:parent #132))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #113)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #111))) :mode nil :granularity nil :parent #107) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #111) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #114) #("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 #117)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #117) #("webqtl" 0 6 (:parent #121))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #117) #("s" 0 1 (:parent #122))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #117)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #117) #("webqtl" 0 6 (:parent #124))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #117) #("plant" 0 5 (:parent #125))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #117))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #114) #("Download one database from\n" 0 27 (:parent #118))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #114) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #119)) #("\n" 0 1 (:parent #119))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #114) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #120))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #114)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #114) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #122))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #114)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #114)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #114) #("and\n" 0 4 (:parent #125))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #114)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #114) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #127))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #114)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #114) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #129))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #114) #("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 #130))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #114) #("Note for the plant database you can rename it to db" 0 51 (:parent #131)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #131) #("webqtl" 0 6 (:parent #135))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #131) #("s" 0 1 (:parent #136))) #(", or\nchange the settings in etc/default" 0 39 (:parent #131)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #131) #("settings.py" 0 11 (:parent #138))) #("to match your path.\n" 0 20 (:parent #131)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #108))) :mode nil :granularity nil :parent #95) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #108) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #111) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #114)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #("\n" 0 1 (:parent #114))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #111)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #109))) :mode nil :granularity nil :parent #95) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #109) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #112) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #115))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #112) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\n" 0 1 (:parent #116))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #110))) :mode nil :granularity nil :parent #95) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #110) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #113) #("See " 0 4 (:parent #116)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #(".\n" 0 2 (:parent #116))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #111))) :mode nil :granularity nil :parent #95) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #111) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #114) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #117)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #117)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #117))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #112))) :mode nil :granularity nil :parent #95) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #115))) :mode section :granularity nil :parent #112) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #115) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #118) #("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 #121)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #121) #("PATH" 0 4 (:parent #125))) #("and R" 0 5 (:parent #121)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #121) #("LIBS" 0 4 (:parent #127))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #121) #("SITE" 0 4 (:parent #128))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #121))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #118)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #118) #("On one system:\n" 0 15 (:parent #123))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #118)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #118) #("and perhaps a few more.\n" 0 24 (:parent #125))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #116)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #116) #("data" 0 4 (:parent #158))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #116)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #116) #("files" 0 5 (:parent #160))) #("/genotype'" 0 10 (:parent #116))) :mode nil :granularity nil :parent #112) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #116) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #119) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #122)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #122) #("data" 0 4 (:parent #126))) #(". 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 #122)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #122) #("settings.py" 0 11 (:parent #128))) #("(see above in\nthis document).\n" 0 30 (:parent #122))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #119) #("You can use the GENENETWORK" 0 27 (:parent #123)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #123) #("FILES" 0 5 (:parent #127))) #("switch to set the datadir, for example\n" 0 39 (:parent #123))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #119)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #117))) :mode nil :granularity nil :parent #112) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #117) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #120) #("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 #123))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #118))) :mode nil :granularity nil :parent #112) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #118) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #121) #("This error\n" 0 11 (:parent #124))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #121)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #121) #("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 #126))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #121) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #127)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #127) #("LIBS" 0 4 (:parent #131))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #127) #("SITE" 0 4 (:parent #132))) #(". 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 #127))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #119))) :mode nil :granularity nil :parent #112) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #119) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #122) #("The following error\n" 0 20 (:parent #125))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #122)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #122) #("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 #127))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #122)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #122) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #129))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #122)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #122) #("if that works run genenetwork after setting SQL" 0 47 (:parent #131)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #131) #("URI" 0 3 (:parent #135))) #("to something like\n" 0 18 (:parent #131))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #122))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #113))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #116))) :mode section :granularity nil :parent #113) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #116) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #119) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #122))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #142) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #145)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #130) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #135) #("Create a gn2 user and home with space\n" 0 38 (:parent #138)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #143) #("add to systemd\n" 0 15 (:parent #146)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #76) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #79) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #82))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #83) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #87) #("A path to the (static) genotype files\n" 0 38 (:parent #90)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #83) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #88) #("Gn-proxy for authentication\n" 0 28 (:parent #91)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #83) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #89) #("The genenetwork3 service\n" 0 25 (:parent #92)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #83) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #90) #("Redis\n" 0 6 (:parent #93)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #83) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #91) #("Mariadb\n" 0 8 (:parent #94))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #77))) :mode nil :granularity nil :parent #70) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #77) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #80) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #83)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #83)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #83))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #80)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #78))) :mode nil :granularity nil :parent #70) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #78) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #81) #("We run a GNU Guix channel with packages at " 0 43 (:parent #84)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #84) #("guix-bioinformatics" 0 19 (:parent #88))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #84)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #84) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #84) #("PATH" 0 4 (:parent #91))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #84))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #81) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #86))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #81) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #88))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #81) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #90))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #81)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #81) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #92)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #92) #("substitutes" 0 11 (:parent #96))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #92)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #92)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #92)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\"` switch.\n" 0 11 (:parent #92))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #81) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #93))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #81)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #81) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #95))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #79) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #82) #("Check out the source with git:\n" 0 31 (:parent #85))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #82)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #82) #("Run GN2 with above Guix profile\n" 0 32 (:parent #87))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #82)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #82) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #89))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #82) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #90))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #82) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #91))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #82) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #92))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #82) #("And browse on your local machine to " 0 36 (:parent #93)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #("\n" 0 1 (:parent #93))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #80))) :mode nil :granularity nil :parent #70) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #80) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #83) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #86)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #86) #("README" 0 6 (:parent #90))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #86))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #81) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #84) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #87))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #82))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #85))) :mode section :granularity nil :parent #82) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #85) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #88) #("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 #91))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #88) #("As root configure the Guix profile\n" 0 35 (:parent #92))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #88) #("and run for example\n" 0 20 (:parent #94))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #88) #("If you want to run as root you may have to set\n" 0 47 (:parent #96))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #88) #("You also need to set\n" 0 21 (:parent #98))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #88) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #100))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #88) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #101))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #88) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #103))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #88) #("When you get errors like:\n" 0 26 (:parent #105))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #88) #("you may need to set\n" 0 20 (:parent #107))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #88)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #86))) :mode nil :granularity nil :parent #82) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #86) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #89) #("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 #92)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #92) #("webqtl" 0 6 (:parent #96))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #92) #("s" 0 1 (:parent #97))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #92)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #92) #("webqtl" 0 6 (:parent #99))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #92) #("plant" 0 5 (:parent #100))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #92))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #89) #("Download one database from\n" 0 27 (:parent #93))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #89) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #94)) #("\n" 0 1 (:parent #94))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #89) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #95))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #89) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #97))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #89)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #89) #("and\n" 0 4 (:parent #100))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #89) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #102))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #89) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #104))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #89) #("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 #105))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #89) #("Note for the plant database you can rename it to db" 0 51 (:parent #106)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #106) #("webqtl" 0 6 (:parent #110))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #106) #("s" 0 1 (:parent #111))) #(", or\nchange the settings in etc/default" 0 39 (:parent #106)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #106) #("settings.py" 0 11 (:parent #113))) #("to match your path.\n" 0 20 (:parent #106)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #83) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #86) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #89)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #("\n" 0 1 (:parent #89))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #86)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #84))) :mode nil :granularity nil :parent #70) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #84) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #87) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #90))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #87) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #("\n" 0 1 (:parent #91))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #85))) :mode nil :granularity nil :parent #70) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #85) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #88) #("See " 0 4 (:parent #91)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #(".\n" 0 2 (:parent #91))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #86))) :mode nil :granularity nil :parent #70) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #86) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #89) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #92)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #92))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #87))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #90))) :mode section :granularity nil :parent #87) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #90) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #93) #("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 #96)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #96) #("PATH" 0 4 (:parent #100))) #("and R" 0 5 (:parent #96)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #96) #("LIBS" 0 4 (:parent #102))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #96) #("SITE" 0 4 (:parent #103))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #96))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #93)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #93) #("On one system:\n" 0 15 (:parent #98))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #93)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #93) #("and perhaps a few more.\n" 0 24 (:parent #100))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #91)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #91) #("data" 0 4 (:parent #133))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #91)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #91) #("files" 0 5 (:parent #135))) #("/genotype'" 0 10 (:parent #91))) :mode nil :granularity nil :parent #87) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #91) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #94) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #97)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #97) #("data" 0 4 (:parent #101))) #(". 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 #97)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #97) #("settings.py" 0 11 (:parent #103))) #("(see above in\nthis document).\n" 0 30 (:parent #97))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #94) #("You can use the GENENETWORK" 0 27 (:parent #98)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #98) #("FILES" 0 5 (:parent #102))) #("switch to set the datadir, for example\n" 0 39 (:parent #98))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #94)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #92))) :mode nil :granularity nil :parent #87) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #92) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #95) #("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 #98))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #93))) :mode nil :granularity nil :parent #87) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #93) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #96) #("This error\n" 0 11 (:parent #99))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #96)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #96) #("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 #101))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #96) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #102)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #102) #("LIBS" 0 4 (:parent #106))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #102) #("SITE" 0 4 (:parent #107))) #(". 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 #102))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #94))) :mode nil :granularity nil :parent #87) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #94) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #97) #("The following error\n" 0 20 (:parent #100))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #97)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #97) #("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 #102))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #97)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #97) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #104))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #97)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #97) #("if that works run genenetwork after setting SQL" 0 47 (:parent #106)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #106) #("URI" 0 3 (:parent #110))) #("to something like\n" 0 18 (:parent #106))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #97))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #88))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #91))) :mode section :granularity nil :parent #88) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #91) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #94) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #97))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #94) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #98) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #101) #("Base install\n" 0 13 (:parent #104))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #101) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #105) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #108) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #111)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #105) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #109) #("Get Guix build going\n" 0 21 (:parent #112))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" 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nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #116) #("Build the correct version of Guix\n" 0 34 (:parent #119)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #117) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #120)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #120)) #("\n" 0 1 (:parent #120)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #118) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #121)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #105) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #110) #("Create a gn2 user and home with space\n" 0 38 (:parent #113)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 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redis\n" 0 14 (:parent #114))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #111) (item (:bullet "- " :begin 12848 :end 12873 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:post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #118) #("add to systemd\n" 0 15 (:parent #121)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #115) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #119) #("update redis.cnf\n" 0 17 (:parent #122)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #115) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #120) #("update database\n" 0 16 (:parent #123)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12926 :tag nil :mode item :granularity nil :parent #105) (paragraph (:begin 12934 :end 12984 :contents-begin 12934 :contents-end 12984 :post-blank 0 :post-affiliated 12934 :mode nil :granularity nil :parent #112) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #115))) (plain-list (:type unordered :begin 12984 :end 13151 :contents-begin 12984 :contents-end 13151 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 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(headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #343) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #347) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #354) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #357)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #378) #("Create a gn2 user and home with space\n" 0 38 (:parent #381)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #386) #("add to systemd\n" 0 15 (:parent #389)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 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#390) #("add to systemd\n" 0 15 (:parent #393))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:begin 121 :end 1439 :contents-begin 121 :contents-end 1438 :robust-begin 121 :robust-end 1436 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1439 :pre-blank 0 :contents-begin 121 :contents-end 1438 :robust-begin 123 :robust-end 1436 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 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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 #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #87))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #76) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #79) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #82))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #83)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #83)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #83))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #80)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #78))) :mode nil :granularity nil :parent #70) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #78) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #81) #("We run a GNU Guix channel with packages at " 0 43 (:parent #84)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #84) #("guix-bioinformatics" 0 19 (:parent #88))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #84)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #84) #("PACKAGE" 0 7 (:parent #90))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #84) #("PATH" 0 4 (:parent #91))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #84))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #81) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #86))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #81) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #88))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #81)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #81) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #90))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #81)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #81) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #92)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #92) #("substitutes" 0 11 (:parent #96))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #92)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #92)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #92)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\"` switch.\n" 0 11 (:parent #92))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #81) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #93))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #81)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #81) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #95))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #79) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #82) #("Check out the source with git:\n" 0 31 (:parent #85))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #82)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #82) #("Run GN2 with above Guix profile\n" 0 32 (:parent #87))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #82)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #82) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #89))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #82) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #90))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #82) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #91))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #82) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #92))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #82) #("And browse on your local machine to " 0 36 (:parent #93)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #("\n" 0 1 (:parent #93))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #80))) :mode nil :granularity nil :parent #70) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #80) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #83) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #86)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #86) #("README" 0 6 (:parent #90))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #86))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #81) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #84) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #87))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #82))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #85))) :mode section :granularity nil :parent #82) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #85) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #88) #("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 #91))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #88) #("As root configure the Guix profile\n" 0 35 (:parent #92))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #88) #("and run for example\n" 0 20 (:parent #94))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #88)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #88) #("If you want to run as root you may have to set\n" 0 47 (:parent #96))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #88) #("You also need to set\n" 0 21 (:parent #98))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #88) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #100))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #88) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #101))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #88) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #103))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #88) #("When you get errors like:\n" 0 26 (:parent #105))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #88)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #88) #("you may need to set\n" 0 20 (:parent #107))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #88)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #86))) :mode nil :granularity nil :parent #82) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #86) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #89) #("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 #92)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #92) #("webqtl" 0 6 (:parent #96))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #92) #("s" 0 1 (:parent #97))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #92)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #92) #("webqtl" 0 6 (:parent #99))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #92) #("plant" 0 5 (:parent #100))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #92))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #89) #("Download one database from\n" 0 27 (:parent #93))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #89) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #94)) #("\n" 0 1 (:parent #94))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #89) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #95))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #89) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #97))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #89)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #89) #("and\n" 0 4 (:parent #100))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #89) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #102))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #89)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #89) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #104))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #89) #("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 #105))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #89) #("Note for the plant database you can rename it to db" 0 51 (:parent #106)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #106) #("webqtl" 0 6 (:parent #110))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #106) #("s" 0 1 (:parent #111))) #(", or\nchange the settings in etc/default" 0 39 (:parent #106)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #106) #("settings.py" 0 11 (:parent #113))) #("to match your path.\n" 0 20 (:parent #106)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #83) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #86) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #89)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #("\n" 0 1 (:parent #89))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #86)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #84))) :mode nil :granularity nil :parent #70) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #84) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #87) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #90))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #87) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #("\n" 0 1 (:parent #91))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #85))) :mode nil :granularity nil :parent #70) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #85) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #88) #("See " 0 4 (:parent #91)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #(".\n" 0 2 (:parent #91))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #86))) :mode nil :granularity nil :parent #70) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #86) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #89) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #92)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #92))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #87))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #90))) :mode section :granularity nil :parent #87) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #90) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #93) #("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 #96)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #96) #("PATH" 0 4 (:parent #100))) #("and R" 0 5 (:parent #96)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #96) #("LIBS" 0 4 (:parent #102))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #96) #("SITE" 0 4 (:parent #103))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #96))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #93)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #93) #("On one system:\n" 0 15 (:parent #98))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #93)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #93) #("and perhaps a few more.\n" 0 24 (:parent #100))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #91)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #91) #("data" 0 4 (:parent #133))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #91)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #91) #("files" 0 5 (:parent #135))) #("/genotype'" 0 10 (:parent #91))) :mode nil :granularity nil :parent #87) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #91) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #94) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #97)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #97) #("data" 0 4 (:parent #101))) #(". 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 #97)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #97) #("settings.py" 0 11 (:parent #103))) #("(see above in\nthis document).\n" 0 30 (:parent #97))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #94) #("You can use the GENENETWORK" 0 27 (:parent #98)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #98) #("FILES" 0 5 (:parent #102))) #("switch to set the datadir, for example\n" 0 39 (:parent #98))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #94)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #92))) :mode nil :granularity nil :parent #87) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #92) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #95) #("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 #98))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #93))) :mode nil :granularity nil :parent #87) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #93) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #96) #("This error\n" 0 11 (:parent #99))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #96)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #96) #("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 #101))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #96) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #102)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #102) #("LIBS" 0 4 (:parent #106))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #102) #("SITE" 0 4 (:parent #107))) #(". 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 #102))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #94))) :mode nil :granularity nil :parent #87) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #94) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #97) #("The following error\n" 0 20 (:parent #100))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #97)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #97) #("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 #102))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #97)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #97) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #104))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #97)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #97) #("if that works run genenetwork after setting SQL" 0 47 (:parent #106)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #106) #("URI" 0 3 (:parent #110))) #("to something like\n" 0 18 (:parent #106))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #97))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #88))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #91))) :mode section :granularity nil :parent #88) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #91) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #94) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #97))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 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(13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #98) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #101) #("Base install\n" 0 13 (:parent #104))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) 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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 #82)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #82) #("Guix-notes" 0 10 (:parent #88))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #82))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #79) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #83) #("Guix bioinformatics" 0 19 (:parent #87))) #("and " 0 4 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #83) #("GNU Guix" 0 8 (:parent #89))) #(".\n" 0 2 (:parent #83))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #79) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #84)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #84) #("GN2 Dependency Graph" 0 20 (:parent #88))) #(".\n" 0 2 (:parent #84))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #77))) :mode nil :granularity nil :parent #71) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #77) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #80) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #83))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #80) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #87) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #90)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #88) #("A path to the (static) genotype files\n" 0 38 (:parent #91)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #89) #("Gn-proxy for authentication\n" 0 28 (:parent #92)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #90) #("The genenetwork3 service\n" 0 25 (:parent #93)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #91) #("Redis\n" 0 6 (:parent #94)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #84) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #92) #("Mariadb\n" 0 8 (:parent #95))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #78))) :mode nil :granularity nil :parent #71) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #78) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #81) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #84)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #84)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #84))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #81)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #79))) :mode nil :granularity nil :parent #71) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #79) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #82) #("We run a GNU Guix channel with packages at " 0 43 (:parent #85)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #85) #("guix-bioinformatics" 0 19 (:parent #89))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #85)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #85) #("PACKAGE" 0 7 (:parent #91))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #85) #("PATH" 0 4 (:parent #92))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #85))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #82)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #82) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #87))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #82)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #82) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #89))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #82)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #82) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #91))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #82)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #82) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #93)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #93) #("substitutes" 0 11 (:parent #97))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #93)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #93)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #93)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #("\"` switch.\n" 0 11 (:parent #93))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #82) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #94))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #82)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #82) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #96))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #80))) :mode nil :granularity nil :parent #71) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #80) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #83) #("Check out the source with git:\n" 0 31 (:parent #86))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #83)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #83) #("Run GN2 with above Guix profile\n" 0 32 (:parent #88))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #83)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #83) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #90))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #83) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #91))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #83) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #92))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #83) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #93))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #83) #("And browse on your local machine to " 0 36 (:parent #94)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #94)) #("\n" 0 1 (:parent #94))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #81))) :mode nil :granularity nil :parent #71) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #81) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #84) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #87)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #87) #("README" 0 6 (:parent #91))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #87))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #82))) :mode nil :granularity nil :parent #71) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #82) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #85) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #88))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #83))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #86))) :mode section :granularity nil :parent #83) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #86) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #89) #("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 #92))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #89) #("As root configure the Guix profile\n" 0 35 (:parent #93))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #89)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #89) #("and run for example\n" 0 20 (:parent #95))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #89)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #89) #("If you want to run as root you may have to set\n" 0 47 (:parent #97))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #89)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #89) #("You also need to set\n" 0 21 (:parent #99))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #89)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #89) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #101))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #89) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #102))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #89)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #89) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #104))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #89)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #89) #("When you get errors like:\n" 0 26 (:parent #106))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #89)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #89) #("you may need to set\n" 0 20 (:parent #108))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #89)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #87))) :mode nil :granularity nil :parent #83) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #87) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #90) #("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 #93)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #93) #("webqtl" 0 6 (:parent #97))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #93) #("s" 0 1 (:parent #98))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #93)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #93) #("webqtl" 0 6 (:parent #100))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #93) #("plant" 0 5 (:parent #101))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #93))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #90) #("Download one database from\n" 0 27 (:parent #94))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #90) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #95)) #("\n" 0 1 (:parent #95))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #90) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #96))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #90)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #90) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #98))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #90)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #90)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #90) #("and\n" 0 4 (:parent #101))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #90)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #90) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #103))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #90)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #90) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #105))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #90) #("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 #106))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #90) #("Note for the plant database you can rename it to db" 0 51 (:parent #107)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #107) #("webqtl" 0 6 (:parent #111))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #107) #("s" 0 1 (:parent #112))) #(", or\nchange the settings in etc/default" 0 39 (:parent #107)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #107) #("settings.py" 0 11 (:parent #114))) #("to match your path.\n" 0 20 (:parent #107)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #84))) :mode nil :granularity nil :parent #71) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #84) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #87) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #90)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #("\n" 0 1 (:parent #90))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #87)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #85))) :mode nil :granularity nil :parent #71) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #85) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #88) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #91))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #88) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\n" 0 1 (:parent #92))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #86))) :mode nil :granularity nil :parent #71) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #86) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #89) #("See " 0 4 (:parent #92)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #(".\n" 0 2 (:parent #92))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #87))) :mode nil :granularity nil :parent #71) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #87) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #90) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #93)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #93))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #88))) :mode nil :granularity nil :parent #71) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #91))) :mode section :granularity nil :parent #88) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #91) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #94) #("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 #97)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #97) #("PATH" 0 4 (:parent #101))) #("and R" 0 5 (:parent #97)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #97) #("LIBS" 0 4 (:parent #103))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #97) #("SITE" 0 4 (:parent #104))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #97))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #94)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #94) #("On one system:\n" 0 15 (:parent #99))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #94)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #94) #("and perhaps a few more.\n" 0 24 (:parent #101))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #92)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #92) #("data" 0 4 (:parent #134))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #92)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #92) #("files" 0 5 (:parent #136))) #("/genotype'" 0 10 (:parent #92))) :mode nil :granularity nil :parent #88) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #92) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #95) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #98)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #98) #("data" 0 4 (:parent #102))) #(". 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 #98)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #98) #("settings.py" 0 11 (:parent #104))) #("(see above in\nthis document).\n" 0 30 (:parent #98))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #95) #("You can use the GENENETWORK" 0 27 (:parent #99)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #99) #("FILES" 0 5 (:parent #103))) #("switch to set the datadir, for example\n" 0 39 (:parent #99))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #95)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #93))) :mode nil :granularity nil :parent #88) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #93) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #96) #("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 #99))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #94))) :mode nil :granularity nil :parent #88) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #94) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #97) #("This error\n" 0 11 (:parent #100))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #97)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #97) #("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 #102))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #97) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #103)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #103) #("LIBS" 0 4 (:parent #107))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #103) #("SITE" 0 4 (:parent #108))) #(". 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 #103))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #95))) :mode nil :granularity nil :parent #88) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #95) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #98) #("The following error\n" 0 20 (:parent #101))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #98)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #98) #("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 #103))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #98)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #98) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #105))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #98)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #98) #("if that works run genenetwork after setting SQL" 0 47 (:parent #107)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #107) #("URI" 0 3 (:parent #111))) #("to something like\n" 0 18 (:parent #107))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #98))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #89))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #92))) :mode section :granularity nil :parent #89) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #92) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #95) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #98))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #95) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #99) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #102) #("Base install\n" 0 13 (:parent #105))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #102) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #106) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #109) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #112)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #106) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #110) #("Get Guix build going\n" 0 21 (:parent #113))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #110) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #114) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #117) #("Build the correct version of Guix\n" 0 34 (:parent #120)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #114) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #118) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #121)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #121)) #("\n" 0 1 (:parent #121)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #114) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #119) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #122)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #106) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #111) #("Create a gn2 user and home with space\n" 0 38 (:parent #114)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #106) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #112) #("Install redis\n" 0 14 (:parent #115))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #112) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #116) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #119) #("add to systemd\n" 0 15 (:parent #122)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #116) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #120) #("update redis.cnf\n" 0 17 (:parent #123)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #116) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #121) #("update database\n" 0 16 (:parent #124)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #51) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #54) #("Large system deployments can get very " 0 38 (:parent #57)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #57) #("complex" 0 7 (:parent #61))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #63))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #58) #("GNU Guix" 0 8 (:parent #64))) #(".\n" 0 2 (:parent #58))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #54) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #59)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #59) #("GN2 Dependency Graph" 0 20 (:parent #63))) #(".\n" 0 2 (:parent #59))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #52) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #55) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #58))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #59) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #66) #("Redis\n" 0 6 (:parent #69)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. 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Follow the instructions on\n" 0 117 (:parent #59)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #59)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #59))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #56)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #54))) :mode nil :granularity nil :parent #46) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #54) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #57) #("We run a GNU Guix channel with packages at " 0 43 (:parent #60)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #60) #("guix-bioinformatics" 0 19 (:parent #64))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #60)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #60) #("PACKAGE" 0 7 (:parent #66))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #60) #("PATH" 0 4 (:parent #67))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #60))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #57) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #62))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #57) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #64))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #57) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #66))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #57)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #57) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #68)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #68) #("substitutes" 0 11 (:parent #72))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #68)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #68)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #68)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #("\"` switch.\n" 0 11 (:parent #68))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #57) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #69))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #57)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #57) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #71))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #55) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #58) #("Check out the source with git:\n" 0 31 (:parent #61))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #58)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #58) #("Run GN2 with above Guix profile\n" 0 32 (:parent #63))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #58)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #58) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #65))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #58) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #66))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #58) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #67))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #58) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #68))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #58) #("And browse on your local machine to " 0 36 (:parent #69)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #69)) #("\n" 0 1 (:parent #69))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #56))) :mode nil :granularity nil :parent #46) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #56) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #59) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #62)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #62) #("README" 0 6 (:parent #66))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #62))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #57) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #60) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #63))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #58))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #61))) :mode section :granularity nil :parent #58) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #61) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #64) #("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 #67))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #64) #("As root configure the Guix profile\n" 0 35 (:parent #68))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #64) #("and run for example\n" 0 20 (:parent #70))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #64) #("If you want to run as root you may have to set\n" 0 47 (:parent #72))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #64) #("You also need to set\n" 0 21 (:parent #74))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #64) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #76))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #64) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #77))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #64) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #79))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #64) #("When you get errors like:\n" 0 26 (:parent #81))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #64) #("you may need to set\n" 0 20 (:parent #83))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #64)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #62))) :mode nil :granularity nil :parent #58) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #62) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #65) #("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 #68)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #68) #("webqtl" 0 6 (:parent #72))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #68) #("s" 0 1 (:parent #73))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #68)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #68) #("webqtl" 0 6 (:parent #75))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #68) #("plant" 0 5 (:parent #76))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #68))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #65) #("Download one database from\n" 0 27 (:parent #69))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #65) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #70)) #("\n" 0 1 (:parent #70))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #65) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #71))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #65) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #73))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #65)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #65) #("and\n" 0 4 (:parent #76))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #65) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #78))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #65) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #80))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #65) #("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 #81))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #65) #("Note for the plant database you can rename it to db" 0 51 (:parent #82)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #82) #("webqtl" 0 6 (:parent #86))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #82) #("s" 0 1 (:parent #87))) #(", or\nchange the settings in etc/default" 0 39 (:parent #82)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #82) #("settings.py" 0 11 (:parent #89))) #("to match your path.\n" 0 20 (:parent #82)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #59) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #62) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #65)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #("\n" 0 1 (:parent #65))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #62)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #60))) :mode nil :granularity nil :parent #46) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #60) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #63) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #66))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #63) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #("\n" 0 1 (:parent #67))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #61))) :mode nil :granularity nil :parent #46) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #61) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #64) #("See " 0 4 (:parent #67)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #(".\n" 0 2 (:parent #67))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #62))) :mode nil :granularity nil :parent #46) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #62) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #65) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #68)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #68))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #63))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #66))) :mode section :granularity nil :parent #63) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #66) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #69) #("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 #72)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #72) #("PATH" 0 4 (:parent #76))) #("and R" 0 5 (:parent #72)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #72) #("LIBS" 0 4 (:parent #78))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #72) #("SITE" 0 4 (:parent #79))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #72))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #69)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #69) #("On one system:\n" 0 15 (:parent #74))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #69)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #69) #("and perhaps a few more.\n" 0 24 (:parent #76))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #67)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #67) #("data" 0 4 (:parent #109))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #67)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #67) #("files" 0 5 (:parent #111))) #("/genotype'" 0 10 (:parent #67))) :mode nil :granularity nil :parent #63) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #67) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #70) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #73)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #73) #("data" 0 4 (:parent #77))) #(". 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 #73)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #73) #("settings.py" 0 11 (:parent #79))) #("(see above in\nthis document).\n" 0 30 (:parent #73))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #70) #("You can use the GENENETWORK" 0 27 (:parent #74)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #74) #("FILES" 0 5 (:parent #78))) #("switch to set the datadir, for example\n" 0 39 (:parent #74))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #70)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #68))) :mode nil :granularity nil :parent #63) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #68) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #71) #("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 #74))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #69))) :mode nil :granularity nil :parent #63) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #69) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #72) #("This error\n" 0 11 (:parent #75))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #72)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #72) #("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 #77))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #72) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #78)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #78) #("LIBS" 0 4 (:parent #82))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #78) #("SITE" 0 4 (:parent #83))) #(". 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 #78))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #70))) :mode nil :granularity nil :parent #63) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #70) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #73) #("The following error\n" 0 20 (:parent #76))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #73)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #73) #("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 #78))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #73)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #73) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #80))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #73)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #73) #("if that works run genenetwork after setting SQL" 0 47 (:parent #82)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #82) #("URI" 0 3 (:parent #86))) #("to something like\n" 0 18 (:parent #82))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #73))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #64))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #67))) :mode section :granularity nil :parent #64) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #67) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #70) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #73))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #70) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #74) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #77) #("Base install\n" 0 13 (:parent #80))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #77) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #81) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #84) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #87)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #81) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #85) #("Get Guix build going\n" 0 21 (:parent #88))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " 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" nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) 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(12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #384) #("Build the correct version of Guix\n" 0 34 (:parent #387)))) (item (:bullet "- " :begin 12575 :end 12702 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:post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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(12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #378) #("Create a gn2 user and home with space\n" 0 38 (:parent #381)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil 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#379) #("Install redis\n" 0 14 (:parent #382))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #379) (item (:bullet "- " :begin 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:contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #386) #("add to systemd\n" 0 15 (:parent #389)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #383) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #387) #("update redis.cnf\n" 0 17 (:parent #390)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #383) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #388) #("update database\n" 0 16 (:parent #391)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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#390) #("add to systemd\n" 0 15 (:parent #393))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((headline (:raw-value "Table of Contents" :begin 43 :end 1439 :pre-blank 0 :contents-begin 121 :contents-end 1438 :robust-begin 123 :robust-end 1436 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #0))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #46) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #49))) #0 (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #51) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #54) #("Large system deployments can get very " 0 38 (:parent #57)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link 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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 #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #63))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #58) #("GNU Guix" 0 8 (:parent #64))) #(".\n" 0 2 (:parent #58))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #54) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #59)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #59) #("GN2 Dependency Graph" 0 20 (:parent #63))) #(".\n" 0 2 (:parent #59))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #52) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #55) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #58))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #59)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #59)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #59))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #56)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #54))) :mode nil :granularity nil :parent #46) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #54) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #57) #("We run a GNU Guix channel with packages at " 0 43 (:parent #60)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #60) #("guix-bioinformatics" 0 19 (:parent #64))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #60)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #60) #("PACKAGE" 0 7 (:parent #66))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #60) #("PATH" 0 4 (:parent #67))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #60))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #57) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #62))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #57) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #64))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #57)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #57) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #66))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #57)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #57) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #68)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #68) #("substitutes" 0 11 (:parent #72))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #68)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #68)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #68)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #("\"` switch.\n" 0 11 (:parent #68))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #57) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #69))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #57)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #57) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #71))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #55) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #58) #("Check out the source with git:\n" 0 31 (:parent #61))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #58)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #58) #("Run GN2 with above Guix profile\n" 0 32 (:parent #63))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #58)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #58) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #65))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #58) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #66))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #58) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #67))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #58) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #68))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #58) #("And browse on your local machine to " 0 36 (:parent #69)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #69)) #("\n" 0 1 (:parent #69))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #56))) :mode nil :granularity nil :parent #46) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #56) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #59) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #62)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #62) #("README" 0 6 (:parent #66))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #62))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #57) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #60) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #63))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #58))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #61))) :mode section :granularity nil :parent #58) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #61) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #64) #("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 #67))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #64) #("As root configure the Guix profile\n" 0 35 (:parent #68))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #64) #("and run for example\n" 0 20 (:parent #70))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #64)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #64) #("If you want to run as root you may have to set\n" 0 47 (:parent #72))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #64) #("You also need to set\n" 0 21 (:parent #74))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #64) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #76))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #64) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #77))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #64) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #79))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #64) #("When you get errors like:\n" 0 26 (:parent #81))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #64)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #64) #("you may need to set\n" 0 20 (:parent #83))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #64)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #62))) :mode nil :granularity nil :parent #58) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #62) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #65) #("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 #68)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #68) #("webqtl" 0 6 (:parent #72))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #68) #("s" 0 1 (:parent #73))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #68)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #68) #("webqtl" 0 6 (:parent #75))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #68) #("plant" 0 5 (:parent #76))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #68))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #65) #("Download one database from\n" 0 27 (:parent #69))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #65) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #70)) #("\n" 0 1 (:parent #70))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #65) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #71))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #65) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #73))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #65)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #65) #("and\n" 0 4 (:parent #76))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #65) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #78))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #65)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #65) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #80))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #65) #("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 #81))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #65) #("Note for the plant database you can rename it to db" 0 51 (:parent #82)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #82) #("webqtl" 0 6 (:parent #86))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #82) #("s" 0 1 (:parent #87))) #(", or\nchange the settings in etc/default" 0 39 (:parent #82)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #82) #("settings.py" 0 11 (:parent #89))) #("to match your path.\n" 0 20 (:parent #82)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #59) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #62) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #65)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #("\n" 0 1 (:parent #65))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #62)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #60))) :mode nil :granularity nil :parent #46) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #60) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #63) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #66))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #63) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #("\n" 0 1 (:parent #67))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #61))) :mode nil :granularity nil :parent #46) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #61) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #64) #("See " 0 4 (:parent #67)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #67)) #(".\n" 0 2 (:parent #67))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #62))) :mode nil :granularity nil :parent #46) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #62) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #65) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #68)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #68))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #63))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #66))) :mode section :granularity nil :parent #63) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #66) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #69) #("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 #72)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #72) #("PATH" 0 4 (:parent #76))) #("and R" 0 5 (:parent #72)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #72) #("LIBS" 0 4 (:parent #78))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #72) #("SITE" 0 4 (:parent #79))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #72))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #69)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #69) #("On one system:\n" 0 15 (:parent #74))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #69)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #69) #("and perhaps a few more.\n" 0 24 (:parent #76))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #67)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #67) #("data" 0 4 (:parent #109))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #67)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #67) #("files" 0 5 (:parent #111))) #("/genotype'" 0 10 (:parent #67))) :mode nil :granularity nil :parent #63) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #67) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #70) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #73)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #73) #("data" 0 4 (:parent #77))) #(". 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 #73)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #73) #("settings.py" 0 11 (:parent #79))) #("(see above in\nthis document).\n" 0 30 (:parent #73))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #70) #("You can use the GENENETWORK" 0 27 (:parent #74)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #74) #("FILES" 0 5 (:parent #78))) #("switch to set the datadir, for example\n" 0 39 (:parent #74))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #70)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #68))) :mode nil :granularity nil :parent #63) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #68) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #71) #("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 #74))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #69))) :mode nil :granularity nil :parent #63) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #69) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #72) #("This error\n" 0 11 (:parent #75))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #72)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #72) #("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 #77))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #72) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #78)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #78) #("LIBS" 0 4 (:parent #82))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #78) #("SITE" 0 4 (:parent #83))) #(". 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 #78))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #70))) :mode nil :granularity nil :parent #63) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #70) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #73) #("The following error\n" 0 20 (:parent #76))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #73)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #73) #("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 #78))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #73)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #73) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #80))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #73)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #73) #("if that works run genenetwork after setting SQL" 0 47 (:parent #82)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #82) #("URI" 0 3 (:parent #86))) #("to something like\n" 0 18 (:parent #82))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #73))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #64))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #67))) :mode section :granularity nil :parent #64) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #67) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #70) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #73))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" 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:granularity nil :parent #94) #("add to systemd\n" 0 15 (:parent #97)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode 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Follow the instructions on\n" 0 117 (:parent #11)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #11)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #11))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #8)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #6))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #6) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #9) #("We run a GNU Guix channel with packages at " 0 43 (:parent #12)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #12) #("guix-bioinformatics" 0 19 (:parent #16))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #12)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #12) #("PACKAGE" 0 7 (:parent #18))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #12) #("PATH" 0 4 (:parent #19))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #12))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #9)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #9) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #14))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #9)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #9) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #16))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #9)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #9) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #18))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #9)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #9) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #20)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #20) #("substitutes" 0 11 (:parent #24))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #20)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #20)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #20)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #20)) #("\"` switch.\n" 0 11 (:parent #20))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #9) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #21))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #9)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #9) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #23))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #7))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #7) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #10) #("Check out the source with git:\n" 0 31 (:parent #13))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #10)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #10) #("Run GN2 with above Guix profile\n" 0 32 (:parent #15))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #10)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #10) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #17))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #10) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #18))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #10) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #19))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #10) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #20))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #10) #("And browse on your local machine to " 0 36 (:parent #21)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #21)) #("\n" 0 1 (:parent #21))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #8))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #8) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #11) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #14)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #14) #("README" 0 6 (:parent #18))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #14))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #9))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #9) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #12) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #15))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #10))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #13))) :mode section :granularity nil :parent #10) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #13) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #16) #("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 #19))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #16) #("As root configure the Guix profile\n" 0 35 (:parent #20))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #16)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #16) #("and run for example\n" 0 20 (:parent #22))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #16)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #16) #("If you want to run as root you may have to set\n" 0 47 (:parent #24))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #16)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #16) #("You also need to set\n" 0 21 (:parent #26))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #16)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #16) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #28))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #16) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #29))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #16)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #16) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #31))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #16)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #16) #("When you get errors like:\n" 0 26 (:parent #33))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #16)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #16) #("you may need to set\n" 0 20 (:parent #35))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #16)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #14))) :mode nil :granularity nil :parent #10) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #14) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #17) #("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 #20)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #20) #("webqtl" 0 6 (:parent #24))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #20) #("s" 0 1 (:parent #25))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #20)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #20) #("webqtl" 0 6 (:parent #27))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #20) #("plant" 0 5 (:parent #28))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #20))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #17) #("Download one database from\n" 0 27 (:parent #21))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #17) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #22)) #("\n" 0 1 (:parent #22))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #17) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #23))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #17)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #17) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #25))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #17)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #17)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #17) #("and\n" 0 4 (:parent #28))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #17)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #17) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #30))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #17)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #17) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #32))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #17) #("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 #33))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #17) #("Note for the plant database you can rename it to db" 0 51 (:parent #34)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #34) #("webqtl" 0 6 (:parent #38))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #34) #("s" 0 1 (:parent #39))) #(", or\nchange the settings in etc/default" 0 39 (:parent #34)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #34) #("settings.py" 0 11 (:parent #41))) #("to match your path.\n" 0 20 (:parent #34)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #11))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #11) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #14) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #17)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #("\n" 0 1 (:parent #17))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #14)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #12))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #12) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #15) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #18))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #15) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #("\n" 0 1 (:parent #19))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #13))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #13) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #16) #("See " 0 4 (:parent #19)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #(".\n" 0 2 (:parent #19))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #14))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #14) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #17) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #20)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #20)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #20))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #15))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #18))) :mode section :granularity nil :parent #15) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #18) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #21) #("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 #24)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #24) #("PATH" 0 4 (:parent #28))) #("and R" 0 5 (:parent #24)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #24) #("LIBS" 0 4 (:parent #30))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #24) #("SITE" 0 4 (:parent #31))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #24))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #21)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #21) #("On one system:\n" 0 15 (:parent #26))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #21)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #21) #("and perhaps a few more.\n" 0 24 (:parent #28))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #19)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #19) #("data" 0 4 (:parent #61))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #19)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #19) #("files" 0 5 (:parent #63))) #("/genotype'" 0 10 (:parent #19))) :mode nil :granularity nil :parent #15) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #19) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #22) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #25)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #25) #("data" 0 4 (:parent #29))) #(". 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 #25)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #25) #("settings.py" 0 11 (:parent #31))) #("(see above in\nthis document).\n" 0 30 (:parent #25))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #22) #("You can use the GENENETWORK" 0 27 (:parent #26)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #26) #("FILES" 0 5 (:parent #30))) #("switch to set the datadir, for example\n" 0 39 (:parent #26))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #22)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #20))) :mode nil :granularity nil :parent #15) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #20) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #23) #("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 #26))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #21))) :mode nil :granularity nil :parent #15) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #21) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #24) #("This error\n" 0 11 (:parent #27))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #24)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #24) #("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 #29))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #24) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #30)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #30) #("LIBS" 0 4 (:parent #34))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #30) #("SITE" 0 4 (:parent #35))) #(". 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 #30))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #22))) :mode nil :granularity nil :parent #15) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #22) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #25) #("The following error\n" 0 20 (:parent #28))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #25)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #25) #("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 #30))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #25)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #25) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #32))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #25)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #25) #("if that works run genenetwork after setting SQL" 0 47 (:parent #34)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #34) #("URI" 0 3 (:parent #38))) #("to something like\n" 0 18 (:parent #34))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #25))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #16))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 13242 :end 13242 :robust-begin 3 :robust-end 13240 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #19))) :mode section :granularity nil :parent #16) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #19) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #22) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #25))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #22) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 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#40))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #37) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #41) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #44) #("Build the correct version of Guix\n" 0 34 (:parent #47)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #41) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #45) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #48)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #48)) #("\n" 0 1 (:parent #48)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #41) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #46) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #49)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #33) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #38) #("Create a gn2 user and home with space\n" 0 38 (:parent #41)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #33) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #39) #("Install redis\n" 0 14 (:parent #42))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 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:post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #46) #("add to systemd\n" 0 15 (:parent #49)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 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4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #48) #("update database\n" 0 16 (:parent #51)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ 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:counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 187) (187 1 "- " nil nil nil 246) (246 1 "- " nil nil nil 311) (311 1 "- " nil nil nil 344) (344 1 "- " nil nil nil 379) (379 1 "- " nil nil nil 408) (408 1 "- " nil nil nil 603) (455 3 "- " nil nil nil 526) (526 3 "- " nil nil nil 603) (603 1 "- " nil nil nil 650) (650 1 "- " nil nil nil 701) (701 1 "- " nil nil nil 776) (776 1 "- " nil nil nil 805) (805 1 "- " nil nil nil 1360) (848 3 "- " nil nil nil 930) (930 3 "- " nil nil nil 1141) (1141 3 "- " nil nil nil 1189) (1189 3 "- " nil nil nil 1254) (1254 3 "- " nil nil nil 1360) (1360 1 "- " nil nil nil 1438) (1381 3 "- " nil nil nil 1438)) :pre-blank 0 :post-blank 0 :post-affiliated 1381 :tag nil :mode item :granularity nil :parent #30) (paragraph (:begin 1386 :end 1438 :contents-begin 1386 :contents-end 1438 :post-blank 0 :post-affiliated 1386 :mode nil :granularity nil :parent #33) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1386 :end 1437 :contents-begin 1413 :contents-end 1435 :post-blank 0 :parent #36) #("Deploying GN2 official" 0 22 (:parent #39))) #("\n" 0 1 (:parent #36))))))))) (headline (:raw-value "Introduction" :begin 1439 :end 2315 :pre-blank 1 :contents-begin 1455 :contents-end 2314 :robust-begin 1457 :robust-end 2312 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1439 :title (#("Introduction" 0 12 (:parent #5))) :mode nil :granularity nil :parent #0) (section (:begin 1455 :end 2315 :contents-begin 1455 :contents-end 2314 :robust-begin 1455 :robust-end 2312 :post-blank 1 :post-affiliated 1455 :mode section :granularity nil :parent #5) (paragraph (:begin 1455 :end 1829 :contents-begin 1455 :contents-end 1828 :post-blank 1 :post-affiliated 1455 :mode planning :granularity nil :parent #8) #("Large system deployments can get very " 0 38 (:parent #11)) (link (:type "http" :path "//genenetwork.org/environments/" :format bracket :raw-link "http://genenetwork.org/environments/" :application nil :search-option nil :begin 1493 :end 1542 :contents-begin 1533 :contents-end 1540 :post-blank 0 :parent #11) #("complex" 0 7 (:parent #15))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #11)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #11) #("Guix-notes" 0 10 (:parent #17))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #11))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #8) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #12) #("Guix bioinformatics" 0 19 (:parent #16))) #("and " 0 4 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #12) #("GNU Guix" 0 8 (:parent #18))) #(".\n" 0 2 (:parent #12))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #8) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #13)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #13) #("GN2 Dependency Graph" 0 20 (:parent #17))) #(".\n" 0 2 (:parent #13))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #6))) :mode nil :granularity nil :parent #0) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #6) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #9) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #12))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #9) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #16) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #19)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #17) #("A path to the (static) genotype files\n" 0 38 (:parent #20)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #18) #("Gn-proxy for authentication\n" 0 28 (:parent #21)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #19) #("The genenetwork3 service\n" 0 25 (:parent #22)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #20) #("Redis\n" 0 6 (:parent #23)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #13) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #21) #("Mariadb\n" 0 8 (:parent #24))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #7))) :mode nil :granularity nil :parent #0) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #7) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #10) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #13)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #13)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #13))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #10)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #8))) :mode nil :granularity nil :parent #0) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #8) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #11) #("We run a GNU Guix channel with packages at " 0 43 (:parent #14)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #14) #("guix-bioinformatics" 0 19 (:parent #18))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #14)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #14) #("PACKAGE" 0 7 (:parent #20))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #14) #("PATH" 0 4 (:parent #21))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #14))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #11)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #11) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #16))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #11)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #11) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #18))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #11)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #11) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #20))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #11)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #11) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #22)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #22) #("substitutes" 0 11 (:parent #26))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #22)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #22)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #22)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #22)) #("\"` switch.\n" 0 11 (:parent #22))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #11) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #23))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #11)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #11) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #25))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #9))) :mode nil :granularity nil :parent #0) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #9) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #12) #("Check out the source with git:\n" 0 31 (:parent #15))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #12)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #12) #("Run GN2 with above Guix profile\n" 0 32 (:parent #17))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #12)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #12) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #19))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #12) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #20))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #12) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #21))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #12) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #22))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #12) #("And browse on your local machine to " 0 36 (:parent #23)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #23)) #("\n" 0 1 (:parent #23))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #10))) :mode nil :granularity nil :parent #0) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #10) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #13) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #16)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #16) #("README" 0 6 (:parent #20))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #16))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #11))) :mode nil :granularity nil :parent #0) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #11) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #14) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #17))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #12))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #15))) :mode section :granularity nil :parent #12) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #15) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #18) #("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 #21))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #18) #("As root configure the Guix profile\n" 0 35 (:parent #22))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #18)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #18) #("and run for example\n" 0 20 (:parent #24))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #18)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #18) #("If you want to run as root you may have to set\n" 0 47 (:parent #26))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #18)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #18) #("You also need to set\n" 0 21 (:parent #28))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #18)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #18) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #30))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #18) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #31))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #18)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #18) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #33))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #18)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #18) #("When you get errors like:\n" 0 26 (:parent #35))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #18)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #18) #("you may need to set\n" 0 20 (:parent #37))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #18)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #16))) :mode nil :granularity nil :parent #12) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #16) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #19) #("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 #22)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #22) #("webqtl" 0 6 (:parent #26))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #22) #("s" 0 1 (:parent #27))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #22)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #22) #("webqtl" 0 6 (:parent #29))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #22) #("plant" 0 5 (:parent #30))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #22))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #19) #("Download one database from\n" 0 27 (:parent #23))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #19) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #24)) #("\n" 0 1 (:parent #24))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #19) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #25))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #19)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #19) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #27))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #19)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #19)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #19) #("and\n" 0 4 (:parent #30))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #19)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #19) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #32))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #19)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #19) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #34))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #19) #("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 #35))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #19) #("Note for the plant database you can rename it to db" 0 51 (:parent #36)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #36) #("webqtl" 0 6 (:parent #40))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #36) #("s" 0 1 (:parent #41))) #(", or\nchange the settings in etc/default" 0 39 (:parent #36)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #36) #("settings.py" 0 11 (:parent #43))) #("to match your path.\n" 0 20 (:parent #36)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #13))) :mode nil :granularity nil :parent #0) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #13) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #16) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #19)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #("\n" 0 1 (:parent #19))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #16)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #14))) :mode nil :granularity nil :parent #0) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #14) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #17) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #20))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #17) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #21)) #("\n" 0 1 (:parent #21))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #15))) :mode nil :granularity nil :parent #0) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #15) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #18) #("See " 0 4 (:parent #21)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #21)) #(".\n" 0 2 (:parent #21))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #16))) :mode nil :granularity nil :parent #0) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #16) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #19) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #22)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #22)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #22))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #17))) :mode nil :granularity nil :parent #0) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #20))) :mode section :granularity nil :parent #17) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #20) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #23) #("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 #26)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #26) #("PATH" 0 4 (:parent #30))) #("and R" 0 5 (:parent #26)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #26) #("LIBS" 0 4 (:parent #32))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #26) #("SITE" 0 4 (:parent #33))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #26))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #23)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #23) #("On one system:\n" 0 15 (:parent #28))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #23)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #23) #("and perhaps a few more.\n" 0 24 (:parent #30))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #21)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #21) #("data" 0 4 (:parent #63))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #21)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #21) #("files" 0 5 (:parent #65))) #("/genotype'" 0 10 (:parent #21))) :mode nil :granularity nil :parent #17) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #21) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #24) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #27)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #27) #("data" 0 4 (:parent #31))) #(". 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 #27)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #27) #("settings.py" 0 11 (:parent #33))) #("(see above in\nthis document).\n" 0 30 (:parent #27))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #24) #("You can use the GENENETWORK" 0 27 (:parent #28)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #28) #("FILES" 0 5 (:parent #32))) #("switch to set the datadir, for example\n" 0 39 (:parent #28))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #24)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #22))) :mode nil :granularity nil :parent #17) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #22) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #25) #("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 #28))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #23))) :mode nil :granularity nil :parent #17) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #23) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #26) #("This error\n" 0 11 (:parent #29))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #26)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #26) #("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 #31))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #26) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #32)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #32) #("LIBS" 0 4 (:parent #36))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #32) #("SITE" 0 4 (:parent #37))) #(". 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 #32))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #24))) :mode nil :granularity nil :parent #17) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #24) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #27) #("The following error\n" 0 20 (:parent #30))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #27)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #27) #("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 #32))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #27)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #27) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #34))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #27)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #27) #("if that works run genenetwork after setting SQL" 0 47 (:parent #36)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #36) #("URI" 0 3 (:parent #40))) #("to something like\n" 0 18 (:parent #36))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #27))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #18))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #21))) :mode section :granularity nil :parent #18) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #21) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #24) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #27))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #24) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #28) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #31) #("Base install\n" 0 13 (:parent #34))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #31) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #35) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #38) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #41)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #35) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #39) #("Get Guix build going\n" 0 21 (:parent #42))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #39) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #46) #("Build the correct version of Guix\n" 0 34 (:parent #49)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #47) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #50)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #50)) #("\n" 0 1 (:parent #50)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #48) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #51)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #35) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #40) #("Create a gn2 user and home with space\n" 0 38 (:parent #43)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #35) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #41) #("Install redis\n" 0 14 (:parent #44))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #41) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 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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 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :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 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :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 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :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 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :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 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #344) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #347) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #350))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :post-blank 0 :post-affiliated 2390 :mode nil :granularity nil :parent #347) (item (:bullet "1. " :begin 2390 :end 2443 :contents-begin 2397 :contents-end 2443 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2390 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2397 :end 2443 :contents-begin 2397 :contents-end 2443 :post-blank 0 :post-affiliated 2397 :mode nil :granularity nil :parent #354) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #357)))) (item (:bullet "1. " :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #355) #("A path to the (static) genotype files\n" 0 38 (:parent #358)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #356) #("Gn-proxy for authentication\n" 0 28 (:parent #359)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #357) #("The genenetwork3 service\n" 0 25 (:parent #360)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #358) #("Redis\n" 0 6 (:parent #361)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #351) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #359) #("Mariadb\n" 0 8 (:parent #362))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #345) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #348) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #351)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #351)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #351))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #348)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #346) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #349) #("We run a GNU Guix channel with packages at " 0 43 (:parent #352)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #352) #("guix-bioinformatics" 0 19 (:parent #356))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #352)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #352) #("PACKAGE" 0 7 (:parent #358))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #352) #("PATH" 0 4 (:parent #359))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #352))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #349) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #354))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #349) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #356))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #349)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #349) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #358))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #349) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #360)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #360) #("substitutes" 0 11 (:parent #364))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #360)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #360)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\"` switch.\n" 0 11 (:parent #360))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #349) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #361))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #349)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #349) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #363))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #347) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #350) #("Check out the source with git:\n" 0 31 (:parent #353))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #350) #("Run GN2 with above Guix profile\n" 0 32 (:parent #355))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #350)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #350) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #357))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #350) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #358))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #350) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #359))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #350) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #360))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #350) #("And browse on your local machine to " 0 36 (:parent #361)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #361)) #("\n" 0 1 (:parent #361))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #348) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #351) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #354)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #354) #("README" 0 6 (:parent #358))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #354))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #349) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #352) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #355))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #350))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :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 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #353))) :mode section :granularity nil :parent #350) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #353) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #356) #("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 #359))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #356) #("As root configure the Guix profile\n" 0 35 (:parent #360))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #356) #("and run for example\n" 0 20 (:parent #362))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #356)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #356) #("If you want to run as root you may have to set\n" 0 47 (:parent #364))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #356) #("You also need to set\n" 0 21 (:parent #366))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #356) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #368))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #356) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #369))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #356) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #371))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #356) #("When you get errors like:\n" 0 26 (:parent #373))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #356)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #356) #("you may need to set\n" 0 20 (:parent #375))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #356)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :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 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #354))) :mode nil :granularity nil :parent #350) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #354) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #364))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #360) #("s" 0 1 (:parent #365))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #360)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #360) #("webqtl" 0 6 (:parent #367))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #360) #("plant" 0 5 (:parent #368))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #360))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #357) #("Download one database from\n" 0 27 (:parent #361))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #357) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #362)) #("\n" 0 1 (:parent #362))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #357) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #363))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #357) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #365))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #357)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #357) #("and\n" 0 4 (:parent #368))) (fixed-width (:begin 8477 :end 8703 :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 8477 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #357) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #370))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #357) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #372))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #357) #("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 #373))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #357) #("Note for the plant database you can rename it to db" 0 51 (:parent #374)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #374) #("webqtl" 0 6 (:parent #378))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #374) #("s" 0 1 (:parent #379))) #(", or\nchange the settings in etc/default" 0 39 (:parent #374)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #374) #("settings.py" 0 11 (:parent #381))) #("to match your path.\n" 0 20 (:parent #374)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #351) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #354) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #357)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #352) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #355) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #358))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #355) (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 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #353))) :mode nil :granularity nil :parent #338) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #353) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #356) #("See " 0 4 (:parent #359)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #(".\n" 0 2 (:parent #359))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #354))) :mode nil :granularity nil :parent #338) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #354) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #357) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #360)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #360))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #355))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :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 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #358))) :mode section :granularity nil :parent #355) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #358) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #361) #("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 #364)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #364) #("PATH" 0 4 (:parent #368))) #("and R" 0 5 (:parent #364)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #364) #("SITE" 0 4 (:parent #371))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #364))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #361) #("On one system:\n" 0 15 (:parent #366))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/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 10222 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #361) #("and perhaps a few more.\n" 0 24 (:parent #368))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :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 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #359)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #359) #("data" 0 4 (:parent #401))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #359)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #359) #("files" 0 5 (:parent #403))) #("/genotype'" 0 10 (:parent #359))) :mode nil :granularity nil :parent #355) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #359) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #362) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #365)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #365) #("data" 0 4 (:parent #369))) #(". 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 #365)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #365) #("settings.py" 0 11 (:parent #371))) #("(see above in\nthis document).\n" 0 30 (:parent #365))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #362) #("You can use the GENENETWORK" 0 27 (:parent #366)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #366) #("FILES" 0 5 (:parent #370))) #("switch to set the datadir, for example\n" 0 39 (:parent #366))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #362)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :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 10930 :title (#("Can't run a module" 0 18 (:parent #360))) :mode nil :granularity nil :parent #355) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #360) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #363) #("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 #366))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :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 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #361))) :mode nil :granularity nil :parent #355) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #361) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #364) #("This error\n" 0 11 (:parent #367))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #364)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #364) #("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 #369))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #364) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #370)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #370) #("LIBS" 0 4 (:parent #374))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #370) #("SITE" 0 4 (:parent #375))) #(". 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 #370))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :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 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #362))) :mode nil :granularity nil :parent #355) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #362) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #365) #("The following error\n" 0 20 (:parent #368))) (fixed-width (:begin 11738 :end 11933 :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 11738 :mode nil :granularity nil :parent #365)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #365) #("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 #370))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #365) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #372))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #365)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #365) #("if that works run genenetwork after setting SQL" 0 47 (:parent #374)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #374) #("URI" 0 3 (:parent #378))) #("to something like\n" 0 18 (:parent #374))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #365))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :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 12330 :title (#("NOTES" 0 5 (:parent #356))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :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 12339 :title (#("Deploying GN2 official" 0 22 (:parent #359))) :mode section :granularity nil :parent #356) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #359) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #362) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #365))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #362) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #366) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #369) #("Base install\n" 0 13 (:parent #372))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #369) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #376) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #379)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #377) #("Get Guix build going\n" 0 21 (:parent #380))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #377) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #384) #("Build the correct version of Guix\n" 0 34 (:parent #387)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #385) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #388)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #388)) #("\n" 0 1 (:parent #388)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #386) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #389)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #378) #("Create a gn2 user and home with space\n" 0 38 (:parent #381)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #373) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #379) #("Install redis\n" 0 14 (:parent #382))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #379) (item (:bullet "- " :begin 12848 :end 12873 :contents-begin 12858 :contents-end 12873 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12848 :tag nil :mode item :granularity nil :parent #383) (paragraph (:begin 12858 :end 12873 :contents-begin 12858 :contents-end 12873 :post-blank 0 :post-affiliated 12858 :mode nil :granularity nil :parent #386) #("add to systemd\n" 0 15 (:parent #389)))) (item (:bullet "- " :begin 12873 :end 12900 :contents-begin 12883 :contents-end 12900 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12873 :tag nil :mode item :granularity nil :parent #383) (paragraph (:begin 12883 :end 12900 :contents-begin 12883 :contents-end 12900 :post-blank 0 :post-affiliated 12883 :mode nil :granularity nil :parent #387) #("update redis.cnf\n" 0 17 (:parent #390)))) (item (:bullet "- " :begin 12900 :end 12926 :contents-begin 12910 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12900 :tag nil :mode item :granularity nil :parent #383) (paragraph (:begin 12910 :end 12926 :contents-begin 12910 :contents-end 12926 :post-blank 0 :post-affiliated 12910 :mode nil :granularity nil :parent #388) #("update database\n" 0 16 (:parent #391)))))) (item (:bullet "+ " :begin 12926 :end 13151 :contents-begin 12934 :contents-end 13151 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 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#390) #("add to systemd\n" 0 15 (:parent #393))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) org-export-as(html nil nil t nil) org-export-to-buffer(html "*Org HTML Export*" nil nil nil t nil #f(compiled-function () #)) org-html-export-as-html(nil nil nil t) (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (let ((temp-buffer (generate-new-buffer " *temp*" t))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))))) eval-buffer(# nil "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t) #f(compiled-function (buffer file) #)(# "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") load-with-code-conversion("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t #f(compiled-function (buffer file) #)) command-line--load-script("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") command-line-1(("-scriptload" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el")) command-line() normal-top-level()