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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 #41)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #42)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #36]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #42))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #43)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #43))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #38]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #44)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #48))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #44)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #44))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #46))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #48))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #41] :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=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #50))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #52)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #56))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #52)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #52))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #53))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #55))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #39]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Check out the source with git:\n" 0 31 (:parent #45))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #47))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #50))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #51))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #52))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And browse on your local machine to " 0 36 (:parent #53)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #40]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #46)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #50))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #46))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #41]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #47))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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Login as root\n" 0 46 (:parent #57))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("and\n" 0 4 (:parent #60))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #62))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #64))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #65))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Note for the plant database you can rename it to db" 0 51 (:parent #66)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("webqtl" 0 6 (:parent #70))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("s" 0 1 (:parent #71))) #(", or\nchange the settings in etc/default" 0 39 (:parent #66)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("settings.py" 0 11 (:parent #73))) #("to match your path.\n" 0 20 (:parent #66)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #43]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The script looks for genotype files. 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The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #52))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #50]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("and R" 0 5 (:parent #56)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #56))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("On one system:\n" 0 15 (:parent #58))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #53] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("and perhaps a few more.\n" 0 24 (:parent #60))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #51)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #63))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #51)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("files" 0 5 (:parent #65))) #("/genotype'" 0 10 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #51]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #57)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("data" 0 4 (:parent #61))) #(". 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 #57)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("(see above in\nthis document).\n" 0 30 (:parent #57))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("You can use the GENENETWORK" 0 27 (:parent #58)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("FILES" 0 5 (:parent #62))) #("switch to set the datadir, for example\n" 0 39 (:parent #58))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #52]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #55]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #62))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #54]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("The following error\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #57] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #62))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #64))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #66)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("URI" 0 3 (:parent #70))) #("to something like\n" 0 18 (:parent #66))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #51]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #57))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). 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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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #376))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #378))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #380)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("URI" 0 3 (:parent #384))) #("to something like\n" 0 18 (:parent #380))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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Debian-derived distros\nmay support\n" 0 117 (:parent #43))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #38]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #44)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #48))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #44)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #44))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #46))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #48))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #41] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #50))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #41] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #52)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #56))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #52)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #52))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #53))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #55))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #39]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Check out the source with git:\n" 0 31 (:parent #45))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #47))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #50))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #51))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #52))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And browse on your local machine to " 0 36 (:parent #53)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #40]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #46)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #50))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #46))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #41]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #47))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #30] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #45]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("As root configure the Guix profile\n" 0 35 (:parent #52))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #48] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("and run for example\n" 0 20 (:parent #54))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #48] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("If you want to run as root you may have to set\n" 0 47 (:parent #56))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("You also need to set\n" 0 21 (:parent #58))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #60))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #61))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #63))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("When you get errors like:\n" 0 26 (:parent #65))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("you may need to set\n" 0 20 (:parent #67))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #46]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("s" 0 1 (:parent #57))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #52)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #59))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("plant" 0 5 (:parent #60))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #52))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Download one database from\n" 0 27 (:parent #53))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #49]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #55))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #49] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #57))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("and\n" 0 4 (:parent #60))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #62))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #64))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #65))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Note for the plant database you can rename it to db" 0 51 (:parent #66)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("webqtl" 0 6 (:parent #70))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("s" 0 1 (:parent #71))) #(", or\nchange the settings in etc/default" 0 39 (:parent #66)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("settings.py" 0 11 (:parent #73))) #("to match your path.\n" 0 20 (:parent #66)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #43]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #49)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #46] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #44]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #50))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #47] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #45]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("See " 0 4 (:parent #51)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #51))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #46]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #52)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #52))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #50]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("and R" 0 5 (:parent #56)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #56))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("On one system:\n" 0 15 (:parent #58))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #53] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("and perhaps a few more.\n" 0 24 (:parent #60))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #51)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #63))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #51)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("files" 0 5 (:parent #65))) #("/genotype'" 0 10 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #51]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #57)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("data" 0 4 (:parent #61))) #(". 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 #57)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("(see above in\nthis document).\n" 0 30 (:parent #57))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("You can use the GENENETWORK" 0 27 (:parent #58)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("FILES" 0 5 (:parent #62))) #("switch to set the datadir, for example\n" 0 39 (:parent #58))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #52]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #55]) #("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. 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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 #62))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #54]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("The following error\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #57] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #62))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #64))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #66)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("URI" 0 3 (:parent #70))) #("to something like\n" 0 18 (:parent #66))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #51]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #57))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #54] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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" 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)) #40] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #50)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("A path to the (static) genotype files\n" 0 38 (:parent #51)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("Gn-proxy for authentication\n" 0 28 (:parent #52)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2530 2530 2530 2555 2555 0 nil nil nil nil nil nil nil nil # nil nil #50]) #("The genenetwork3 service\n" 0 25 (:parent #53)))) (item (:standard-properties [2555 2555 2562 2568 2568 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2562 2562 2562 2568 2568 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("Redis\n" 0 6 (:parent #54)))) (item (:standard-properties [2568 2568 2575 2583 2583 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #44] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2575 2575 2575 2583 2583 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("Mariadb\n" 0 8 (:parent #55))))))) (headline (:standard-properties [2584 2584 2612 2909 2909 0 (:title) nil nil nil nil 2614 2907 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 26) t] :title (#("Installing Guix packages" 0 24 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2612 2612 2612 2909 2909 0 nil section nil nil nil 2612 2909 nil # nil nil #38]) (paragraph (:standard-properties [2612 2612 2612 2884 2885 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #44)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #44))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #39]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #45)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #49))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #45)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #51))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #45))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #47))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #51))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #53)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #57))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #53)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #53))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #54))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #56))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #40]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Check out the source with git:\n" 0 31 (:parent #46))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #48))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #43] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #50))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #51))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #52))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #53))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("And browse on your local machine to " 0 36 (:parent #54)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #41]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #47)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #51))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #47))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #42]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #48))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #31] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #46]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("As root configure the Guix profile\n" 0 35 (:parent #53))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #49] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("and run for example\n" 0 20 (:parent #55))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #49] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("If you want to run as root you may have to set\n" 0 47 (:parent #57))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You also need to set\n" 0 21 (:parent #59))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #61))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #62))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #64))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("When you get errors like:\n" 0 26 (:parent #66))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("you may need to set\n" 0 20 (:parent #68))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #47]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("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 #53)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("webqtl" 0 6 (:parent #57))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("s" 0 1 (:parent #58))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #53)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("webqtl" 0 6 (:parent #60))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("plant" 0 5 (:parent #61))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #53))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Download one database from\n" 0 27 (:parent #54))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #50]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #55))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #56))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #50] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #58))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("and\n" 0 4 (:parent #61))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #63))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #65))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("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 #66))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Note for the plant database you can rename it to db" 0 51 (:parent #67)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("webqtl" 0 6 (:parent #71))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("s" 0 1 (:parent #72))) #(", or\nchange the settings in etc/default" 0 39 (:parent #67)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("settings.py" 0 11 (:parent #74))) #("to match your path.\n" 0 20 (:parent #67)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #44]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #50)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #47] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #45]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #51))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #48] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #46]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("See " 0 4 (:parent #52)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #52))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #47]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #53)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #53))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #51]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("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 #57)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("and R" 0 5 (:parent #57)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("LIBS" 0 4 (:parent #63))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("SITE" 0 4 (:parent #64))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #57))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("On one system:\n" 0 15 (:parent #59))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #54] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("and perhaps a few more.\n" 0 24 (:parent #61))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #52)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #64))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #52)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("files" 0 5 (:parent #66))) #("/genotype'" 0 10 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #52]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #58)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("data" 0 4 (:parent #62))) #(". 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 #58)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("settings.py" 0 11 (:parent #64))) #("(see above in\nthis document).\n" 0 30 (:parent #58))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("You can use the GENENETWORK" 0 27 (:parent #59)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("FILES" 0 5 (:parent #63))) #("switch to set the datadir, for example\n" 0 39 (:parent #59))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #53]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #56]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #63))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #55]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #58]) #("The following error\n" 0 20 (:parent #61))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #58] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("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 #63))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #58] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #65))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #58] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #67)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("URI" 0 3 (:parent #71))) #("to something like\n" 0 18 (:parent #67))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #58] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #49))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #52]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #58))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #41)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #42)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #36]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #42))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #43)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #43))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #38]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #44)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #48))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #44)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #44))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #46))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #48))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #41] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #50))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #41] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #52)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #56))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #52)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #52))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #53))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #55))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #39]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Check out the source with git:\n" 0 31 (:parent #45))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #47))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #50))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #51))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #52))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And browse on your local machine to " 0 36 (:parent #53)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #40]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #46)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #50))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #46))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #41]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #47))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #30] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # 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nil nil #48] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #63))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("When you get errors like:\n" 0 26 (:parent #65))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("you may need to set\n" 0 20 (:parent #67))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #46]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("s" 0 1 (:parent #57))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #52)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #59))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("plant" 0 5 (:parent #60))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #52))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Download one database from\n" 0 27 (:parent #53))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #49]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #55))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #49] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #57))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("and\n" 0 4 (:parent #60))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #62))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #64))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #65))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Note for the plant database you can rename it to db" 0 51 (:parent #66)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("webqtl" 0 6 (:parent #70))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("s" 0 1 (:parent #71))) #(", or\nchange the settings in etc/default" 0 39 (:parent #66)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("settings.py" 0 11 (:parent #73))) #("to match your path.\n" 0 20 (:parent #66)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #43]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #49)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #46] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #44]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #50))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #47] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #45]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("See " 0 4 (:parent #51)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #51))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #46]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #52)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #52))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #50]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("and R" 0 5 (:parent #56)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #56))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("On one system:\n" 0 15 (:parent #58))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #53] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("and perhaps a few more.\n" 0 24 (:parent #60))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #51)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #63))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #51)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("files" 0 5 (:parent #65))) #("/genotype'" 0 10 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #51]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #57)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("data" 0 4 (:parent #61))) #(". 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 #57)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("(see above in\nthis document).\n" 0 30 (:parent #57))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("You can use the GENENETWORK" 0 27 (:parent #58)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("FILES" 0 5 (:parent #62))) #("switch to set the datadir, for example\n" 0 39 (:parent #58))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #52]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #55]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #62))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #54]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("The following error\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #57] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("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 #62))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #64))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #66)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("URI" 0 3 (:parent #70))) #("to something like\n" 0 18 (:parent #66))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #51]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #57))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #54] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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" 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)) #34] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #41]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #44)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #42]) #("A path to the (static) genotype files\n" 0 38 (:parent #45)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("Gn-proxy for authentication\n" 0 28 (:parent #46)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2530 2530 2530 2555 2555 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("The genenetwork3 service\n" 0 25 (:parent #47)))) (item (:standard-properties [2555 2555 2562 2568 2568 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2562 2562 2562 2568 2568 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("Redis\n" 0 6 (:parent #48)))) (item (:standard-properties [2568 2568 2575 2583 2583 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #38] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2575 2575 2575 2583 2583 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("Mariadb\n" 0 8 (:parent #49))))))) (headline (:standard-properties [2584 2584 2612 2909 2909 0 (:title) nil nil nil nil 2614 2907 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 26) t] :title (#("Installing Guix packages" 0 24 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2612 2612 2612 2909 2909 0 nil section nil nil nil 2612 2909 nil # nil nil #32]) (paragraph (:standard-properties [2612 2612 2612 2884 2885 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #38)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #38))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #33]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #39)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #43))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #39)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #45))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #39))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #41))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #43))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #45))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #47)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #51))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #47)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #47))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #48))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #50))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #34]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Check out the source with git:\n" 0 31 (:parent #40))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #42))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #37] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #45))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #46))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #47))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("And browse on your local machine to " 0 36 (:parent #48)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #35]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #41)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #45))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #41))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #36]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #42))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #40]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("As root configure the Guix profile\n" 0 35 (:parent #47))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #43] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("and run for example\n" 0 20 (:parent #49))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you want to run as root you may have to set\n" 0 47 (:parent #51))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You also need to set\n" 0 21 (:parent #53))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #55))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #56))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #58))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("When you get errors like:\n" 0 26 (:parent #60))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("you may need to set\n" 0 20 (:parent #62))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #41]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("s" 0 1 (:parent #52))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #47)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("plant" 0 5 (:parent #55))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #47))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Download one database from\n" 0 27 (:parent #48))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #44]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #50))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #52))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and\n" 0 4 (:parent #55))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #57))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #59))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #60))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note for the plant database you can rename it to db" 0 51 (:parent #61)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("webqtl" 0 6 (:parent #65))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("s" 0 1 (:parent #66))) #(", or\nchange the settings in etc/default" 0 39 (:parent #61)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("settings.py" 0 11 (:parent #68))) #("to match your path.\n" 0 20 (:parent #61)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #38]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #44)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #39]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #45))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #42] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #40]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("See " 0 4 (:parent #46)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #41]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #47)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #47))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #45]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("and R" 0 5 (:parent #51)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #51))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("On one system:\n" 0 15 (:parent #53))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #48] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("and perhaps a few more.\n" 0 24 (:parent #55))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #46)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #46)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("files" 0 5 (:parent #60))) #("/genotype'" 0 10 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #46]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #52)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #(". 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 #52)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("(see above in\nthis document).\n" 0 30 (:parent #52))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You can use the GENENETWORK" 0 27 (:parent #53)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("FILES" 0 5 (:parent #57))) #("switch to set the datadir, for example\n" 0 39 (:parent #53))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #47]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #50]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #57))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #49]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("The following error\n" 0 20 (:parent #55))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #52] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #52] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #46]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #52))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #53] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12428 12428 12428 12441 12441 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("Base install\n" 0 13 (:parent #59))) (plain-list (:standard-properties [12441 12441 12441 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #56] :type unordered) (item (:standard-properties [12441 12441 12449 12502 12502 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12449 12449 12449 12502 12502 0 nil nil nil nil nil nil nil nil # nil nil #63]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #66)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #64]) #("Get Guix build going\n" 0 21 (:parent #67))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #68] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12541 12541 12541 12575 12575 0 nil nil nil nil nil nil nil nil # nil nil #71]) #("Build the correct version of Guix\n" 0 34 (:parent #74)))) (item (:standard-properties [12575 12575 12585 12702 12702 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #68] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12585 12585 12585 12702 12702 0 nil nil nil nil nil nil nil nil # nil nil #72]) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #75)) (link (:standard-properties [12648 nil nil nil 12701 0 nil nil nil nil nil nil nil nil # nil nil #75] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #75)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #68] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # nil nil #73]) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #76)))))) (item (:standard-properties [12780 12780 12788 12826 12826 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12788 12788 12788 12826 12826 0 nil nil nil nil nil nil nil nil # nil nil #65]) #("Create a gn2 user and home with space\n" 0 38 (:parent #68)))) (item (:standard-properties [12826 12826 12834 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12834 12834 12834 12848 12848 0 nil nil nil nil nil nil nil nil # nil nil #66]) #("Install redis\n" 0 14 (:parent #69))) (plain-list (:standard-properties [12848 12848 12848 12926 12926 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #66] :type unordered) (item (:standard-properties [12848 12848 12858 12873 12873 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #70] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12858 12858 12858 12873 12873 0 nil nil nil nil nil nil nil nil # nil nil #73]) #("add to systemd\n" 0 15 (:parent #76)))) (item (:standard-properties [12873 12873 12883 12900 12900 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #70] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12883 12883 12883 12900 12900 0 nil nil nil nil nil nil nil nil # nil nil #74]) #("update redis.cnf\n" 0 17 (:parent #77)))) (item (:standard-properties [12900 12900 12910 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #70] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12910 12910 12910 12926 12926 0 nil nil nil nil nil nil nil nil # nil nil #75]) #("update database\n" 0 16 (:parent #78)))))) (item (:standard-properties [12926 12926 12934 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12934 12934 12934 12984 12984 0 nil nil nil nil nil nil nil nil # nil nil #67]) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #70))) (plain-list (:standard-properties [12984 12984 12984 13151 13151 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #67] :type unordered) (item (:standard-properties [12984 12984 12994 13009 13009 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #71] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12994 12994 12994 13009 13009 0 nil nil nil nil nil nil nil nil # nil nil #74]) #("add to systemd\n" 0 15 (:parent #77)))) (item (:standard-properties [13009 13009 13019 13037 13037 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #71] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13019 13019 13019 13037 13037 0 nil nil nil nil nil nil nil nil # nil nil #75]) #("system stop mysql\n" 0 18 (:parent #78)))) (item (:standard-properties [13037 13037 13047 13064 13064 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "[ ]" 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((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)) #353] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #360]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #363)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #361]) #("A path to the (static) genotype files\n" 0 38 (:parent #364)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Gn-proxy for authentication\n" 0 28 (:parent #365)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #357)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #357))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #352]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #358)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #358] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #362))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #360))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #362))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #364))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #356] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #359))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #359]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("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 #365))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("As root configure the Guix profile\n" 0 35 (:parent #366))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #362] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("and run for example\n" 0 20 (:parent #368))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #362] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("If you want to run as root you may have to set\n" 0 47 (:parent #370))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("You also need to set\n" 0 21 (:parent #372))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #374))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #375))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #377))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("When you get errors like:\n" 0 26 (:parent #379))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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You can find them in\n" 0 58 (:parent #363)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #363] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #363))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #360] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #358]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #364))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #361] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #359))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #359]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("See " 0 4 (:parent #365)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #365))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #360))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #360]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #366)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #382]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #385)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #379] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #383]) #("Get Guix build going\n" 0 21 (:parent #386))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #383] :type unordered) (item (:standard-properties [12531 12531 12541 12575 12575 0 (:tag) item nil nil nil nil nil nil # 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nil nil #394] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #394)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #387] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #43))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #45))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #47)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #51))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #47)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #47))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #48))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #50))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #34]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Check out the source with git:\n" 0 31 (:parent #40))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #42))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #37] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #45))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #46))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #47))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("And browse on your local machine to " 0 36 (:parent #48)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #35]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #41)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #45))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #41))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #36]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #42))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #40]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("As root configure the Guix profile\n" 0 35 (:parent #47))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #43] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("and run for example\n" 0 20 (:parent #49))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you want to run as root you may have to set\n" 0 47 (:parent #51))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You also need to set\n" 0 21 (:parent #53))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #55))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #56))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #58))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("When you get errors like:\n" 0 26 (:parent #60))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("you may need to set\n" 0 20 (:parent #62))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #41]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("s" 0 1 (:parent #52))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #47)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("plant" 0 5 (:parent #55))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #47))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Download one database from\n" 0 27 (:parent #48))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #44]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #50))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #52))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and\n" 0 4 (:parent #55))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #57))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #59))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #60))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note for the plant database you can rename it to db" 0 51 (:parent #61)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("webqtl" 0 6 (:parent #65))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("s" 0 1 (:parent #66))) #(", or\nchange the settings in etc/default" 0 39 (:parent #61)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("settings.py" 0 11 (:parent #68))) #("to match your path.\n" 0 20 (:parent #61)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #38]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #44)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #39]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #45))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #42] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #40]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("See " 0 4 (:parent #46)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #41]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #47)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #47))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #45]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("and R" 0 5 (:parent #51)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #51))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("On one system:\n" 0 15 (:parent #53))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #48] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("and perhaps a few more.\n" 0 24 (:parent #55))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #46)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #46)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("files" 0 5 (:parent #60))) #("/genotype'" 0 10 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #46]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #52)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #(". 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 #52)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("(see above in\nthis document).\n" 0 30 (:parent #52))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You can use the GENENETWORK" 0 27 (:parent #53)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("FILES" 0 5 (:parent #57))) #("switch to set the datadir, for example\n" 0 39 (:parent #53))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #47]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #50]) #("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 #53))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #48]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("This error\n" 0 11 (:parent #54))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("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 #56))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #57)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("LIBS" 0 4 (:parent #61))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("SITE" 0 4 (:parent #62))) #(". 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 #57))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #49]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("The following error\n" 0 20 (:parent #55))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #52] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #57))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #59))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #61)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("URI" 0 3 (:parent #65))) #("to something like\n" 0 18 (:parent #61))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #46]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #52))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #49] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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Debian-derived distros\nmay support\n" 0 117 (:parent #39))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #34]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #40)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #44))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #40)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #46))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PATH" 0 4 (:parent #47))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #40))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #42))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #37] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #46))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #37] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #48)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #52))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #48)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #48))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #49))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #37] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #51))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #35]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Check out the source with git:\n" 0 31 (:parent #41))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #43))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #38] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #45))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #46))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #47))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #38]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #48))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("And browse on your local machine to " 0 36 (:parent #49)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #36]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #42)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #46))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #42))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #37]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #43))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #26] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #41]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("As root configure the Guix profile\n" 0 35 (:parent #48))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #44] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and run for example\n" 0 20 (:parent #50))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("If you want to run as root you may have to set\n" 0 47 (:parent #52))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You also need to set\n" 0 21 (:parent #54))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #56))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #57))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #59))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("When you get errors like:\n" 0 26 (:parent #61))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("you may need to set\n" 0 20 (:parent #63))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #42]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("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 #48)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("webqtl" 0 6 (:parent #52))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("s" 0 1 (:parent #53))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #48)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("webqtl" 0 6 (:parent #55))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("plant" 0 5 (:parent #56))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #48))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Download one database from\n" 0 27 (:parent #49))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #45]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #51))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #53))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("and\n" 0 4 (:parent #56))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #58))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #60))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #61))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Note for the plant database you can rename it to db" 0 51 (:parent #62)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("webqtl" 0 6 (:parent #66))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("s" 0 1 (:parent #67))) #(", or\nchange the settings in etc/default" 0 39 (:parent #62)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("settings.py" 0 11 (:parent #69))) #("to match your path.\n" 0 20 (:parent #62)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #39]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #45)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #40]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #46))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #41]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("See " 0 4 (:parent #47)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #42]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #46]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #47]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". 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 #53)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #48]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("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. 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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 #58))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #50]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The following error\n" 0 20 (:parent #56))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #53] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("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 #58))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #60))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #62)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("URI" 0 3 (:parent #66))) #("to something like\n" 0 18 (:parent #62))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #47]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #53))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #34)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #40))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("PATH" 0 4 (:parent #41))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #34))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("It should upgrade (ignore the locales warnings). 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #38))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #31] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #40))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #31] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #42)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #46))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #42)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #42))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #43))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #31] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #45))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #29]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Check out the source with git:\n" 0 31 (:parent #35))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #37))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #32] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #39))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #40))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #41))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #42))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("And browse on your local machine to " 0 36 (:parent #43)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #30]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #36)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #40))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #36))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #31]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #37))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #20] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #35]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("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 #41))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("As root configure the Guix profile\n" 0 35 (:parent #42))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #38] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("and run for example\n" 0 20 (:parent #44))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you want to run as root you may have to set\n" 0 47 (:parent #46))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("You also need to set\n" 0 21 (:parent #48))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #50))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #51))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #53))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("When you get errors like:\n" 0 26 (:parent #55))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("you may need to set\n" 0 20 (:parent #57))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #36]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("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 #42)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #46))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("s" 0 1 (:parent #47))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #42)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("plant" 0 5 (:parent #50))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #42))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Download one database from\n" 0 27 (:parent #43))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #39]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #45))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #47))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("and\n" 0 4 (:parent #50))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #52))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #54))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #55))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note for the plant database you can rename it to db" 0 51 (:parent #56)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("webqtl" 0 6 (:parent #60))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("s" 0 1 (:parent #61))) #(", or\nchange the settings in etc/default" 0 39 (:parent #56)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("to match your path.\n" 0 20 (:parent #56)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #33]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #39)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #34]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #40))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #37] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #41))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #35]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("See " 0 4 (:parent #41)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #41))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #36]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #42)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #42))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #40]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("and R" 0 5 (:parent #46)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("LIBS" 0 4 (:parent #52))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("SITE" 0 4 (:parent #53))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #46))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("On one system:\n" 0 15 (:parent #48))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #43] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("and perhaps a few more.\n" 0 24 (:parent #50))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #41)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #41)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("files" 0 5 (:parent #55))) #("/genotype'" 0 10 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #41]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #47)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #51))) #(". 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 #47)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #53))) #("(see above in\nthis document).\n" 0 30 (:parent #47))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You can use the GENENETWORK" 0 27 (:parent #48)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("FILES" 0 5 (:parent #52))) #("switch to set the datadir, for example\n" 0 39 (:parent #48))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #42]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #45]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #52))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #44]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The following error\n" 0 20 (:parent #50))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #47] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #47] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #41]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #47))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #48] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12428 12428 12428 12441 12441 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("Base install\n" 0 13 (:parent #54))) (plain-list (:standard-properties [12441 12441 12441 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :type unordered) (item (:standard-properties [12441 12441 12449 12502 12502 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12449 12449 12449 12502 12502 0 nil nil nil nil nil nil nil nil # nil nil #58]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #61)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #59]) #("Get Guix build going\n" 0 21 (:parent #62))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #63] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12541 12541 12541 12575 12575 0 nil nil nil nil nil nil nil nil # nil nil #66]) #("Build the correct version of Guix\n" 0 34 (:parent #69)))) (item (:standard-properties [12575 12575 12585 12702 12702 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #63] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12585 12585 12585 12702 12702 0 nil nil nil nil nil nil nil nil # nil nil #67]) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #70)) (link (:standard-properties [12648 nil nil nil 12701 0 nil nil nil nil nil nil nil nil # nil nil #70] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #70)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #63] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # nil nil #68]) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #71)))))) (item (:standard-properties [12780 12780 12788 12826 12826 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12788 12788 12788 12826 12826 0 nil nil nil nil nil nil nil nil # nil nil #60]) #("Create a gn2 user and home with space\n" 0 38 (:parent #63)))) (item (:standard-properties [12826 12826 12834 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12834 12834 12834 12848 12848 0 nil nil nil nil nil nil nil nil # nil nil #61]) #("Install redis\n" 0 14 (:parent #64))) (plain-list (:standard-properties [12848 12848 12848 12926 12926 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #61] :type unordered) (item (:standard-properties [12848 12848 12858 12873 12873 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #65] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12858 12858 12858 12873 12873 0 nil nil nil nil nil nil nil nil # nil nil #68]) #("add to systemd\n" 0 15 (:parent #71)))) (item (:standard-properties [12873 12873 12883 12900 12900 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #65] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12883 12883 12883 12900 12900 0 nil nil nil nil nil nil nil nil # nil nil #69]) #("update redis.cnf\n" 0 17 (:parent #72)))) (item (:standard-properties [12900 12900 12910 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #65] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12910 12910 12910 12926 12926 0 nil nil nil nil nil nil nil nil # nil nil #70]) #("update database\n" 0 16 (:parent #73)))))) (item (:standard-properties [12926 12926 12934 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12934 12934 12934 12984 12984 0 nil nil nil nil nil nil nil nil # nil nil #62]) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #65))) (plain-list (:standard-properties [12984 12984 12984 13151 13151 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #62] :type unordered) (item (:standard-properties [12984 12984 12994 13009 13009 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #66] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12994 12994 12994 13009 13009 0 nil nil nil nil nil nil nil nil # nil nil #69]) #("add to systemd\n" 0 15 (:parent #72)))) (item (:standard-properties [13009 13009 13019 13037 13037 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #66] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13019 13019 13019 13037 13037 0 nil nil nil nil nil nil nil nil # nil nil #70]) #("system stop mysql\n" 0 18 (:parent #73)))) (item (:standard-properties [13037 13037 13047 13064 13064 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "[ ]" 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((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)) #353] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #360]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #363)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #361]) #("A path to the (static) genotype files\n" 0 38 (:parent #364)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Gn-proxy for authentication\n" 0 28 (:parent #365)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #357)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #357))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #352]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #358)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #358] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #362))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #360))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #362))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #364))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #356] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #359))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #359]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("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 #365))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("As root configure the Guix profile\n" 0 35 (:parent #366))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #362] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("and run for example\n" 0 20 (:parent #368))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #362] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("If you want to run as root you may have to set\n" 0 47 (:parent #370))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("You also need to set\n" 0 21 (:parent #372))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #374))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #375))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #377))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("When you get errors like:\n" 0 26 (:parent #379))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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You can find them in\n" 0 58 (:parent #363)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #363] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #363))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #360] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #358]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #364))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #361] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #359))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #359]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("See " 0 4 (:parent #365)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #365))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #360))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #360]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #366)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #382]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #385)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #379] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #383]) #("Get Guix build going\n" 0 21 (:parent #386))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #383] :type unordered) (item (:standard-properties [12531 12531 12541 12575 12575 0 (:tag) item nil nil nil nil nil nil # 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nil nil #394] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #394)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #387] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #38))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #31] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #40))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #31] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #42)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #46))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #42)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #42))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #43))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #31] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #45))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #29]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Check out the source with git:\n" 0 31 (:parent #35))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #37))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #32] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #39))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #40))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #41))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #32]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #42))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("And browse on your local machine to " 0 36 (:parent #43)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #30]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #36)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #40))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #36))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #31]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #37))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #20] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #35]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("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 #41))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("As root configure the Guix profile\n" 0 35 (:parent #42))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #38] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("and run for example\n" 0 20 (:parent #44))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you want to run as root you may have to set\n" 0 47 (:parent #46))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("You also need to set\n" 0 21 (:parent #48))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #50))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #51))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #53))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("When you get errors like:\n" 0 26 (:parent #55))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("you may need to set\n" 0 20 (:parent #57))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #36]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("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 #42)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #46))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("s" 0 1 (:parent #47))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #42)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("plant" 0 5 (:parent #50))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #42))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Download one database from\n" 0 27 (:parent #43))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #39]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #45))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #47))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("and\n" 0 4 (:parent #50))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #52))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #54))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #55))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Note for the plant database you can rename it to db" 0 51 (:parent #56)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("webqtl" 0 6 (:parent #60))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("s" 0 1 (:parent #61))) #(", or\nchange the settings in etc/default" 0 39 (:parent #56)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("to match your path.\n" 0 20 (:parent #56)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #33]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #39)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #34]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #40))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #37] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #41))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #35]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("See " 0 4 (:parent #41)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #41))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #36]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #42)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #42))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #40]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #50))) #("and R" 0 5 (:parent #46)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("LIBS" 0 4 (:parent #52))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("SITE" 0 4 (:parent #53))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #46))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("On one system:\n" 0 15 (:parent #48))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #43] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("and perhaps a few more.\n" 0 24 (:parent #50))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #41)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #41)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("files" 0 5 (:parent #55))) #("/genotype'" 0 10 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #41]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #47)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #51))) #(". 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 #47)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("settings.py" 0 11 (:parent #53))) #("(see above in\nthis document).\n" 0 30 (:parent #47))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You can use the GENENETWORK" 0 27 (:parent #48)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("FILES" 0 5 (:parent #52))) #("switch to set the datadir, for example\n" 0 39 (:parent #48))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #42]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #45]) #("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 #48))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #43]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("This error\n" 0 11 (:parent #49))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("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 #51))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #52)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #56))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #57))) #(". 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 #52))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #44]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The following error\n" 0 20 (:parent #50))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #47] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #52))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #54))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #56)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("URI" 0 3 (:parent #60))) #("to something like\n" 0 18 (:parent #56))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #20] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #41]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #47))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #44] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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Debian-derived distros\nmay support\n" 0 117 (:parent #34))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #29]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #35)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #39))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #35)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #41))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #35] :use-brackets-p nil) #("PATH" 0 4 (:parent #42))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #35))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #37))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #39))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #32] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #41))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #32] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #43)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #47))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #43)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #43))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #44))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #32] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #46))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #30]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Check out the source with git:\n" 0 31 (:parent #36))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #38))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #33] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #40))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #41))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #42))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #33]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #43))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("And browse on your local machine to " 0 36 (:parent #44)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #31]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #37)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #41))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #37))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #32]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #38))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #21] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #36]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("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 #42))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("As root configure the Guix profile\n" 0 35 (:parent #43))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #39] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("and run for example\n" 0 20 (:parent #45))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you want to run as root you may have to set\n" 0 47 (:parent #47))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You also need to set\n" 0 21 (:parent #49))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #51))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #52))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #54))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("When you get errors like:\n" 0 26 (:parent #56))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("you may need to set\n" 0 20 (:parent #58))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #37]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("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 #43)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("webqtl" 0 6 (:parent #47))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("s" 0 1 (:parent #48))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #43)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("webqtl" 0 6 (:parent #50))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("plant" 0 5 (:parent #51))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #43))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Download one database from\n" 0 27 (:parent #44))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #40]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #46))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #48))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and\n" 0 4 (:parent #51))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #53))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #55))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("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 #56))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Note for the plant database you can rename it to db" 0 51 (:parent #57)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("webqtl" 0 6 (:parent #61))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("s" 0 1 (:parent #62))) #(", or\nchange the settings in etc/default" 0 39 (:parent #57)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #64))) #("to match your path.\n" 0 20 (:parent #57)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #34]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #40)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #40))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #37] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #35]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #41))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #38] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #36]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("See " 0 4 (:parent #42)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #42))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #37]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #43)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #43))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #41]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("and R" 0 5 (:parent #47)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("LIBS" 0 4 (:parent #53))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("SITE" 0 4 (:parent #54))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #47))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("On one system:\n" 0 15 (:parent #49))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #44] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("and perhaps a few more.\n" 0 24 (:parent #51))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #42)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #42)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("files" 0 5 (:parent #56))) #("/genotype'" 0 10 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #42]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #48)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #52))) #(". 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 #48)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("settings.py" 0 11 (:parent #54))) #("(see above in\nthis document).\n" 0 30 (:parent #48))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You can use the GENENETWORK" 0 27 (:parent #49)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("FILES" 0 5 (:parent #53))) #("switch to set the datadir, for example\n" 0 39 (:parent #49))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #43]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #46]) #("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. 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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 #53))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #45]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The following error\n" 0 20 (:parent #51))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #48] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("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 #53))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #55))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #57)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("URI" 0 3 (:parent #61))) #("to something like\n" 0 18 (:parent #57))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #21] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #42]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #48))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #33)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #39))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #33))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #30]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #40))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #33] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #42))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #33] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #44)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #48))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #44)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #44))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #45))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #33] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("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 #47))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #31]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Check out the source with git:\n" 0 31 (:parent #37))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #39))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #34] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #41))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #42))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #43))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #34]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #44))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("And browse on your local machine to " 0 36 (:parent #45)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #32]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #38)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #42))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #38))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #33]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #39))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #22] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #37]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("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 #43))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("As root configure the Guix profile\n" 0 35 (:parent #44))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #40] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("and run for example\n" 0 20 (:parent #46))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("If you want to run as root you may have to set\n" 0 47 (:parent #48))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You also need to set\n" 0 21 (:parent #50))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #52))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #53))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #55))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("When you get errors like:\n" 0 26 (:parent #57))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("you may need to set\n" 0 20 (:parent #59))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #38]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("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 #44)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #48))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("s" 0 1 (:parent #49))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #44)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("plant" 0 5 (:parent #52))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #44))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Download one database from\n" 0 27 (:parent #45))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #41]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #47))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #49))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and\n" 0 4 (:parent #52))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #54))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #56))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #57))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Note for the plant database you can rename it to db" 0 51 (:parent #58)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("webqtl" 0 6 (:parent #62))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("s" 0 1 (:parent #63))) #(", or\nchange the settings in etc/default" 0 39 (:parent #58)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("settings.py" 0 11 (:parent #65))) #("to match your path.\n" 0 20 (:parent #58)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #35]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #41)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #41))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #36]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #42))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #39] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #37]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("See " 0 4 (:parent #43)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #38]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #44)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #44))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #42]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("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 #48)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("and R" 0 5 (:parent #48)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("LIBS" 0 4 (:parent #54))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("SITE" 0 4 (:parent #55))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #48))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("On one system:\n" 0 15 (:parent #50))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #45] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("and perhaps a few more.\n" 0 24 (:parent #52))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #43)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #55))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #43)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("files" 0 5 (:parent #57))) #("/genotype'" 0 10 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #43]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #49)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("data" 0 4 (:parent #53))) #(". 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 #49)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("settings.py" 0 11 (:parent #55))) #("(see above in\nthis document).\n" 0 30 (:parent #49))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You can use the GENENETWORK" 0 27 (:parent #50)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("FILES" 0 5 (:parent #54))) #("switch to set the datadir, for example\n" 0 39 (:parent #50))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #44]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #47]) #("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 #50))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #45]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("This error\n" 0 11 (:parent #51))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("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 #53))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #54)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #(". 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 #54))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #39] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #46]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The following error\n" 0 20 (:parent #52))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #54))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #56))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #58)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("URI" 0 3 (:parent #62))) #("to something like\n" 0 18 (:parent #58))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #43]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #49))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #46] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #23]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #26] :key "TITLE" :value "Installing GeneNetwork services"))) #18 (headline (:standard-properties [1439 1439 1455 2315 2315 0 (:title) nil nil nil nil 1457 2313 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1455 1455 1455 2315 2315 0 nil section nil nil nil 1455 2315 nil # nil nil #28]) (paragraph (:standard-properties [1455 1455 1455 1828 1829 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("Large system deployments can get very " 0 38 (:parent #34)) (link (:standard-properties [1493 nil 1533 1540 1542 0 nil nil nil nil nil nil 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 #34)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #40))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #34))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #35)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #39))) #("and " 0 4 (:parent #35)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #41))) #(".\n" 0 2 (:parent #35))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #36)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #40))) #(".\n" 0 2 (:parent #36))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #29]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #35))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #37)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #43))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("PATH" 0 4 (:parent #44))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #37))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #39))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). 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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 #45)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #49))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #45)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #45))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #46))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #34] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #48))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #32]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("Check out the source with git:\n" 0 31 (:parent #38))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #40))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #35] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("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 #42))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #43))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #44))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #35]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #45))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("And browse on your local machine to " 0 36 (:parent #46)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #33]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #39)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #43))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #39))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #34]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #40))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #23] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #38]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("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 #44))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("As root configure the Guix profile\n" 0 35 (:parent #45))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #41] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("and run for example\n" 0 20 (:parent #47))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # 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nil nil #41] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #56))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("When you get errors like:\n" 0 26 (:parent #58))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("you may need to set\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #35] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #39]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("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 #45)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("webqtl" 0 6 (:parent #49))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("s" 0 1 (:parent #50))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #45)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("webqtl" 0 6 (:parent #52))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("plant" 0 5 (:parent #53))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #45))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Download one database from\n" 0 27 (:parent #46))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #42]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #48))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #50))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("and\n" 0 4 (:parent #53))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #55))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #57))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #58))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Note for the plant database you can rename it to db" 0 51 (:parent #59)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("webqtl" 0 6 (:parent #63))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("s" 0 1 (:parent #64))) #(", or\nchange the settings in etc/default" 0 39 (:parent #59)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("settings.py" 0 11 (:parent #66))) #("to match your path.\n" 0 20 (:parent #59)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #36]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #42)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #42))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #37]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #43))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #40] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #38]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("See " 0 4 (:parent #44)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #44))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #39]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #45)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #45))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #43]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("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 #49)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("and R" 0 5 (:parent #49)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("LIBS" 0 4 (:parent #55))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("SITE" 0 4 (:parent #56))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #49))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("On one system:\n" 0 15 (:parent #51))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #46] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("and perhaps a few more.\n" 0 24 (:parent #53))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #44)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #44)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("files" 0 5 (:parent #58))) #("/genotype'" 0 10 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #44]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #50)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("data" 0 4 (:parent #54))) #(". 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 #50)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("settings.py" 0 11 (:parent #56))) #("(see above in\nthis document).\n" 0 30 (:parent #50))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("You can use the GENENETWORK" 0 27 (:parent #51)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("FILES" 0 5 (:parent #55))) #("switch to set the datadir, for example\n" 0 39 (:parent #51))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #45]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #46]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("This error\n" 0 11 (:parent #52))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #54))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #55)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("LIBS" 0 4 (:parent #59))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("SITE" 0 4 (:parent #60))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. 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nil nil #50] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #38)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #44))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("PATH" 0 4 (:parent #45))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #38))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("It should upgrade (ignore the locales warnings). 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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 #46)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #50))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #46)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #46))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("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 #47))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #35] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("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 #49))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #33]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("Check out the source with git:\n" 0 31 (:parent #39))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #41))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #43))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #44))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #45))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #36]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #46))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("And browse on your local machine to " 0 36 (:parent #47)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #34]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #40)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #44))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #40))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #35]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #41))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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nil nil #42] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #57))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("When you get errors like:\n" 0 26 (:parent #59))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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Login as root\n" 0 46 (:parent #51))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("and\n" 0 4 (:parent #54))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #56))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #58))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #59))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Note for the plant database you can rename it to db" 0 51 (:parent #60)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("webqtl" 0 6 (:parent #64))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("s" 0 1 (:parent #65))) #(", or\nchange the settings in etc/default" 0 39 (:parent #60)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("settings.py" 0 11 (:parent #67))) #("to match your path.\n" 0 20 (:parent #60)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #37]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #43)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #43))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #38]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #44))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #41] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #39]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("See " 0 4 (:parent #45)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #45))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #40]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #46)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #46))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #44]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("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 #50)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("and R" 0 5 (:parent #50)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("LIBS" 0 4 (:parent #56))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("SITE" 0 4 (:parent #57))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #50))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("On one system:\n" 0 15 (:parent #52))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #47] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("and perhaps a few more.\n" 0 24 (:parent #54))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #45)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #45)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("files" 0 5 (:parent #59))) #("/genotype'" 0 10 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #45]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #51)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #55))) #(". 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 #51)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("settings.py" 0 11 (:parent #57))) #("(see above in\nthis document).\n" 0 30 (:parent #51))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("You can use the GENENETWORK" 0 27 (:parent #52)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("FILES" 0 5 (:parent #56))) #("switch to set the datadir, for example\n" 0 39 (:parent #52))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #46]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #49]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #56))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #48]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("The following error\n" 0 20 (:parent #54))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #51] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #51] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #24] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #45]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #51))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #48] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #36)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #42))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #36))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #43))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #45))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #36] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #47)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #51))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #47)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #47))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #48))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #36] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #50))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #34]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("Check out the source with git:\n" 0 31 (:parent #40))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #42))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #37] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #44))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #45))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #46))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #37]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #47))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("And browse on your local machine to " 0 36 (:parent #48)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #35]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #41)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #45))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #41))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #36]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #42))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #25] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #40]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("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 #46))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("As root configure the Guix profile\n" 0 35 (:parent #47))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #43] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("and run for example\n" 0 20 (:parent #49))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you want to run as root you may have to set\n" 0 47 (:parent #51))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("You also need to set\n" 0 21 (:parent #53))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #55))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #56))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #58))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("When you get errors like:\n" 0 26 (:parent #60))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("you may need to set\n" 0 20 (:parent #62))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #37] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #41]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #51))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("s" 0 1 (:parent #52))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #47)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("plant" 0 5 (:parent #55))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #47))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Download one database from\n" 0 27 (:parent #48))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #44]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #50))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #52))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and\n" 0 4 (:parent #55))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #57))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #59))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #60))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Note for the plant database you can rename it to db" 0 51 (:parent #61)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("webqtl" 0 6 (:parent #65))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("s" 0 1 (:parent #66))) #(", or\nchange the settings in etc/default" 0 39 (:parent #61)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("settings.py" 0 11 (:parent #68))) #("to match your path.\n" 0 20 (:parent #61)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #38]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #44)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #44))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #39]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #45))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #42] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #40]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("See " 0 4 (:parent #46)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #41]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #47)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #47))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #45]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("and R" 0 5 (:parent #51)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("LIBS" 0 4 (:parent #57))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("SITE" 0 4 (:parent #58))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #51))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("On one system:\n" 0 15 (:parent #53))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #48] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("and perhaps a few more.\n" 0 24 (:parent #55))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #46)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #46)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("files" 0 5 (:parent #60))) #("/genotype'" 0 10 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #46]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #52)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #56))) #(". 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 #52)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("(see above in\nthis document).\n" 0 30 (:parent #52))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You can use the GENENETWORK" 0 27 (:parent #53)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("FILES" 0 5 (:parent #57))) #("switch to set the datadir, for example\n" 0 39 (:parent #53))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #47]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #50]) #("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 #53))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #48]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("This error\n" 0 11 (:parent #54))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("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 #56))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #57)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("LIBS" 0 4 (:parent #61))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("SITE" 0 4 (:parent #62))) #(". 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 #57))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #49]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("The following error\n" 0 20 (:parent #55))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #52] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #57))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #59))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #61)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("URI" 0 3 (:parent #65))) #("to something like\n" 0 18 (:parent #61))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #25] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #46]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #52))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #49] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #37)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #43))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #37))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #38)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #42))) #("and " 0 4 (:parent #38)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #44))) #(".\n" 0 2 (:parent #38))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #39)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #43))) #(".\n" 0 2 (:parent #39))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #32]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #38))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #40)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #46))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #40] :use-brackets-p nil) #("PATH" 0 4 (:parent #47))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #40))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #42))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). 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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 #48)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #52))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #48)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #48))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #49))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #37] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #51))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #35]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Check out the source with git:\n" 0 31 (:parent #41))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #43))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #38] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #45))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #46))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #47))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #38]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #48))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("And browse on your local machine to " 0 36 (:parent #49)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #36]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #42)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #46))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #42))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #37]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #43))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #26] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #41))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #41]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("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 #47))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("As root configure the Guix profile\n" 0 35 (:parent #48))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #44] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("and run for example\n" 0 20 (:parent #50))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # 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nil nil #44] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #59))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("When you get errors like:\n" 0 26 (:parent #61))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("you may need to set\n" 0 20 (:parent #63))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #38] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #42))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #42]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("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 #48)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("webqtl" 0 6 (:parent #52))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("s" 0 1 (:parent #53))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #48)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("webqtl" 0 6 (:parent #55))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("plant" 0 5 (:parent #56))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #48))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Download one database from\n" 0 27 (:parent #49))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #45]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #51))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #53))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("and\n" 0 4 (:parent #56))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #58))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #60))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #61))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Note for the plant database you can rename it to db" 0 51 (:parent #62)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("webqtl" 0 6 (:parent #66))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("s" 0 1 (:parent #67))) #(", or\nchange the settings in etc/default" 0 39 (:parent #62)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("settings.py" 0 11 (:parent #69))) #("to match your path.\n" 0 20 (:parent #62)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #39]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #45)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #45))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #40]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #46))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #43] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #41]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("See " 0 4 (:parent #47)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #47))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #42]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #48)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #48))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #46]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #56))) #("and R" 0 5 (:parent #52)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("LIBS" 0 4 (:parent #58))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("SITE" 0 4 (:parent #59))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #52))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("On one system:\n" 0 15 (:parent #54))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #49] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("and perhaps a few more.\n" 0 24 (:parent #56))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #47)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #47)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #47]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #53)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #57))) #(". 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 #53)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("(see above in\nthis document).\n" 0 30 (:parent #53))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You can use the GENENETWORK" 0 27 (:parent #54)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("FILES" 0 5 (:parent #58))) #("switch to set the datadir, for example\n" 0 39 (:parent #54))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #48]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #51]) #("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 #54))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #43] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #49]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("This error\n" 0 11 (:parent #55))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #57))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #58)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. 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nil nil #53] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #26] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #41)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #47))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PATH" 0 4 (:parent #48))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #41))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("It should upgrade (ignore the locales warnings). 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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 #49)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #53))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #49)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #49))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #50))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #38] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #52))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #36]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Check out the source with git:\n" 0 31 (:parent #42))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #44))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #39] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #46))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #47))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #48))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #39]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #49))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("And browse on your local machine to " 0 36 (:parent #50)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #37]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #43)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #47))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #43))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #38]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #44))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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nil nil #45] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #60))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("When you get errors like:\n" 0 26 (:parent #62))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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Login as root\n" 0 46 (:parent #54))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and\n" 0 4 (:parent #57))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #59))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #61))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("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 #62))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Note for the plant database you can rename it to db" 0 51 (:parent #63)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #63] :use-brackets-p nil) #("webqtl" 0 6 (:parent #67))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #63] :use-brackets-p nil) #("s" 0 1 (:parent #68))) #(", or\nchange the settings in etc/default" 0 39 (:parent #63)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #63] :use-brackets-p nil) #("settings.py" 0 11 (:parent #70))) #("to match your path.\n" 0 20 (:parent #63)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #40]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #46)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #46))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #41]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #47))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #44] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #42]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("See " 0 4 (:parent #48)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #48))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #43]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #49)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #49))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #47]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("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 #53)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("PATH" 0 4 (:parent #57))) #("and R" 0 5 (:parent #53)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("LIBS" 0 4 (:parent #59))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("SITE" 0 4 (:parent #60))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #53))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("On one system:\n" 0 15 (:parent #55))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #50] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #50]) #("and perhaps a few more.\n" 0 24 (:parent #57))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #48)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("data" 0 4 (:parent #60))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #48)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("files" 0 5 (:parent #62))) #("/genotype'" 0 10 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #48]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #54)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("data" 0 4 (:parent #58))) #(". 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 #54)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("settings.py" 0 11 (:parent #60))) #("(see above in\nthis document).\n" 0 30 (:parent #54))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("You can use the GENENETWORK" 0 27 (:parent #55)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("FILES" 0 5 (:parent #59))) #("switch to set the datadir, for example\n" 0 39 (:parent #55))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #49]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #52]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #59))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #51]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The following error\n" 0 20 (:parent #57))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #54] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #54] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #48]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #54))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #39)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #45))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #39))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #46))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #39] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #48))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #39] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #50)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #54))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #50)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #50))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #51))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #39] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("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 #53))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #37]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Check out the source with git:\n" 0 31 (:parent #43))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #45))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #40] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("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 #47))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #48))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #49))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #40]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #50))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("And browse on your local machine to " 0 36 (:parent #51)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #38]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #44)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #48))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #44))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #39]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #45))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #28] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #43))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #43]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("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 #49))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("As root configure the Guix profile\n" 0 35 (:parent #50))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #46] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("and run for example\n" 0 20 (:parent #52))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #46] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("If you want to run as root you may have to set\n" 0 47 (:parent #54))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("You also need to set\n" 0 21 (:parent #56))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #58))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #59))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #61))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("When you get errors like:\n" 0 26 (:parent #63))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("you may need to set\n" 0 20 (:parent #65))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #40] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #44]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("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 #50)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("webqtl" 0 6 (:parent #54))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("s" 0 1 (:parent #55))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #50)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("webqtl" 0 6 (:parent #57))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("plant" 0 5 (:parent #58))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #50))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Download one database from\n" 0 27 (:parent #51))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #47]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #53))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #47] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #55))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("and\n" 0 4 (:parent #58))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #60))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #62))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("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 #63))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Note for the plant database you can rename it to db" 0 51 (:parent #64)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("webqtl" 0 6 (:parent #68))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("s" 0 1 (:parent #69))) #(", or\nchange the settings in etc/default" 0 39 (:parent #64)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("settings.py" 0 11 (:parent #71))) #("to match your path.\n" 0 20 (:parent #64)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #41]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #47)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #47))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #42]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #48))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #45] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #43]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("See " 0 4 (:parent #49)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #49))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #44]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #50)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #50))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #48]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("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 #54)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("and R" 0 5 (:parent #54)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("LIBS" 0 4 (:parent #60))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("SITE" 0 4 (:parent #61))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #54))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("On one system:\n" 0 15 (:parent #56))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #51] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("and perhaps a few more.\n" 0 24 (:parent #58))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #49)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("data" 0 4 (:parent #61))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #49)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("files" 0 5 (:parent #63))) #("/genotype'" 0 10 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #49]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #55)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("data" 0 4 (:parent #59))) #(". 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 #55)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("settings.py" 0 11 (:parent #61))) #("(see above in\nthis document).\n" 0 30 (:parent #55))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("You can use the GENENETWORK" 0 27 (:parent #56)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("FILES" 0 5 (:parent #60))) #("switch to set the datadir, for example\n" 0 39 (:parent #56))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #50]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #51]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("This error\n" 0 11 (:parent #57))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("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 #59))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #60)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("LIBS" 0 4 (:parent #64))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("SITE" 0 4 (:parent #65))) #(". 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 #60))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #52]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("The following error\n" 0 20 (:parent #58))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #55] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("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 #60))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #62))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #64)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("URI" 0 3 (:parent #68))) #("to something like\n" 0 18 (:parent #64))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #49]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #55))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #52] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #40)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #46))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #40))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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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 #51)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #55))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #51)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #51))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("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 #52))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("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 #54))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #38]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("Check out the source with git:\n" 0 31 (:parent #44))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #46))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #41] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #48))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #49))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #50))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #41]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #51))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("And browse on your local machine to " 0 36 (:parent #52)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #39]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #45)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #49))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #45))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #40]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #46))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #29] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #44))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #44]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("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 #50))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("As root configure the Guix profile\n" 0 35 (:parent #51))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #47] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("and run for example\n" 0 20 (:parent #53))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #47] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("If you want to run as root you may have to set\n" 0 47 (:parent #55))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("You also need to set\n" 0 21 (:parent #57))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #59))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #60))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #62))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("When you get errors like:\n" 0 26 (:parent #64))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #47]) #("you may need to set\n" 0 20 (:parent #66))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #47] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #41] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #45]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("webqtl" 0 6 (:parent #55))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("s" 0 1 (:parent #56))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #51)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("webqtl" 0 6 (:parent #58))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("plant" 0 5 (:parent #59))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #51))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Download one database from\n" 0 27 (:parent #52))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #48]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #54))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #48] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #56))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("and\n" 0 4 (:parent #59))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #61))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #63))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("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 #64))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Note for the plant database you can rename it to db" 0 51 (:parent #65)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("webqtl" 0 6 (:parent #69))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("s" 0 1 (:parent #70))) #(", or\nchange the settings in etc/default" 0 39 (:parent #65)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("settings.py" 0 11 (:parent #72))) #("to match your path.\n" 0 20 (:parent #65)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #42]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #48)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #48))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #43]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #49))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #46] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #44]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("See " 0 4 (:parent #50)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #50))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #45]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #51)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #51))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #49]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("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 #55)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("and R" 0 5 (:parent #55)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("LIBS" 0 4 (:parent #61))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("SITE" 0 4 (:parent #62))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #55))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("On one system:\n" 0 15 (:parent #57))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #52] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("and perhaps a few more.\n" 0 24 (:parent #59))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #50)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("data" 0 4 (:parent #62))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #50)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("files" 0 5 (:parent #64))) #("/genotype'" 0 10 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #50]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #56)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("data" 0 4 (:parent #60))) #(". 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 #56)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("settings.py" 0 11 (:parent #62))) #("(see above in\nthis document).\n" 0 30 (:parent #56))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("You can use the GENENETWORK" 0 27 (:parent #57)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("FILES" 0 5 (:parent #61))) #("switch to set the datadir, for example\n" 0 39 (:parent #57))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #51]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #54]) #("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 #57))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #52]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("This error\n" 0 11 (:parent #58))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("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 #60))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #61)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("LIBS" 0 4 (:parent #65))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("SITE" 0 4 (:parent #66))) #(". 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 #61))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #53]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #56]) #("The following error\n" 0 20 (:parent #59))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #56] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("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 #61))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #63))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #65)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("URI" 0 3 (:parent #69))) #("to something like\n" 0 18 (:parent #65))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #50]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #56))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #53] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #30]) (keyword (:standard-properties [1 1 nil nil 43 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services"))) #25 (headline (:standard-properties [1439 1439 1455 2315 2315 0 (:title) nil nil nil nil 1457 2313 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1455 1455 1455 2315 2315 0 nil section nil nil nil 1455 2315 nil # nil nil #35]) (paragraph (:standard-properties [1455 1455 1455 1828 1829 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments can get very " 0 38 (:parent #41)) (link (:standard-properties [1493 nil 1533 1540 1542 0 nil nil nil nil nil nil 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 #41)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #47))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #41))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("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 #42)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #46))) #("and " 0 4 (:parent #42)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #48))) #(".\n" 0 2 (:parent #42))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #43)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #47))) #(".\n" 0 2 (:parent #43))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #36]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #42))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #44)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #50))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("PATH" 0 4 (:parent #51))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #44))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #46))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). 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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 #52)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #56))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #52)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #52))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #53))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #55))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #39]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("Check out the source with git:\n" 0 31 (:parent #45))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #47))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #42] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #49))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #50))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #51))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #42]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #52))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("And browse on your local machine to " 0 36 (:parent #53)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #40]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #46)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #50))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #46))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #41]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #47))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #30] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #45))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #45]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("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 #51))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("As root configure the Guix profile\n" 0 35 (:parent #52))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #48] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("and run for example\n" 0 20 (:parent #54))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #48] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # 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nil nil #48] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #63))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("When you get errors like:\n" 0 26 (:parent #65))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #48]) #("you may need to set\n" 0 20 (:parent #67))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #48] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #42] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #46))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #46]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("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 #52)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("s" 0 1 (:parent #57))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #52)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #59))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("plant" 0 5 (:parent #60))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #52))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Download one database from\n" 0 27 (:parent #53))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #49]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #55))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #49] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #57))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("and\n" 0 4 (:parent #60))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #62))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #64))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("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 #65))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Note for the plant database you can rename it to db" 0 51 (:parent #66)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("webqtl" 0 6 (:parent #70))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("s" 0 1 (:parent #71))) #(", or\nchange the settings in etc/default" 0 39 (:parent #66)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("settings.py" 0 11 (:parent #73))) #("to match your path.\n" 0 20 (:parent #66)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #43]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #49)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #49))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #46] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #44]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #50))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #47] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #45]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("See " 0 4 (:parent #51)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #51))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #46]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #52)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #52))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #50]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("PATH" 0 4 (:parent #60))) #("and R" 0 5 (:parent #56)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("LIBS" 0 4 (:parent #62))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("SITE" 0 4 (:parent #63))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #56))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("On one system:\n" 0 15 (:parent #58))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #53] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("and perhaps a few more.\n" 0 24 (:parent #60))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #51)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("data" 0 4 (:parent #63))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #51)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("files" 0 5 (:parent #65))) #("/genotype'" 0 10 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #51]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #57)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("data" 0 4 (:parent #61))) #(". 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 #57)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("settings.py" 0 11 (:parent #63))) #("(see above in\nthis document).\n" 0 30 (:parent #57))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("You can use the GENENETWORK" 0 27 (:parent #58)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("FILES" 0 5 (:parent #62))) #("switch to set the datadir, for example\n" 0 39 (:parent #58))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #52]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #55]) #("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 #58))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #53]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #56]) #("This error\n" 0 11 (:parent #59))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("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 #61))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #62)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("LIBS" 0 4 (:parent #66))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("SITE" 0 4 (:parent #67))) #(". 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 #62))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #47] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #54]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("The following error\n" 0 20 (:parent #60))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #57] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #57] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #45)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #51))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #45] :use-brackets-p nil) #("PATH" 0 4 (:parent #52))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #45))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("It should upgrade (ignore the locales warnings). 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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 #53)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #57))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #53)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #53))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #54))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #42] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #56))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #40))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #40]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("Check out the source with git:\n" 0 31 (:parent #46))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #48))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #43] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #50))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #51))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #52))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #43]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #53))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("And browse on your local machine to " 0 36 (:parent #54)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #41]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #47)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #47] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #51))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #47))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #42]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #48))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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nil nil #49] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #64))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #49]) #("When you get errors like:\n" 0 26 (:parent #66))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #49] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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Login as root\n" 0 46 (:parent #58))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("and\n" 0 4 (:parent #61))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #63))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #65))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("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 #66))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Note for the plant database you can rename it to db" 0 51 (:parent #67)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("webqtl" 0 6 (:parent #71))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("s" 0 1 (:parent #72))) #(", or\nchange the settings in etc/default" 0 39 (:parent #67)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #67] :use-brackets-p nil) #("settings.py" 0 11 (:parent #74))) #("to match your path.\n" 0 20 (:parent #67)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #44]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #50)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #50))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #47] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #45]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #51))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #48] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #46]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("See " 0 4 (:parent #52)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #52))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #47]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #53)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #53))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #51))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #51]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #54]) #("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 #57)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("PATH" 0 4 (:parent #61))) #("and R" 0 5 (:parent #57)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("LIBS" 0 4 (:parent #63))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #57] :use-brackets-p nil) #("SITE" 0 4 (:parent #64))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #57))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #54] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #54]) #("On one system:\n" 0 15 (:parent #59))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #54] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("and perhaps a few more.\n" 0 24 (:parent #61))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #52)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("data" 0 4 (:parent #64))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #52)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("files" 0 5 (:parent #66))) #("/genotype'" 0 10 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #52]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #58)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("data" 0 4 (:parent #62))) #(". 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 #58)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("settings.py" 0 11 (:parent #64))) #("(see above in\nthis document).\n" 0 30 (:parent #58))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("You can use the GENENETWORK" 0 27 (:parent #59)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("FILES" 0 5 (:parent #63))) #("switch to set the datadir, for example\n" 0 39 (:parent #59))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #53]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #56]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #63))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #48] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #55]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #58]) #("The following error\n" 0 20 (:parent #61))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #58] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #58] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #49))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #52]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #58))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #43)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #49))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #43))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #46)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #52))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("PATH" 0 4 (:parent #53))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #46))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #43] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("It should upgrade (ignore the locales warnings). 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #50))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #43] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #52))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #43] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #54)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #58))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #54)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #54] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #54))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #55))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #43] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("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 #57))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #41))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #41]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #44]) #("Check out the source with git:\n" 0 31 (:parent #47))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #49))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #44] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #51))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #52))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #53))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #44]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #54))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("And browse on your local machine to " 0 36 (:parent #55)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #55))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #42]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #48)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #48] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #52))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #48))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #43]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #49))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #32] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #47))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #47]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("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 #53))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("As root configure the Guix profile\n" 0 35 (:parent #54))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #50] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("and run for example\n" 0 20 (:parent #56))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #50] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("If you want to run as root you may have to set\n" 0 47 (:parent #58))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("You also need to set\n" 0 21 (:parent #60))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #62))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #63))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #65))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("When you get errors like:\n" 0 26 (:parent #67))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #50]) #("you may need to set\n" 0 20 (:parent #69))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #50] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #44] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #48]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("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 #54)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("webqtl" 0 6 (:parent #58))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("s" 0 1 (:parent #59))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #54)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("webqtl" 0 6 (:parent #61))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("plant" 0 5 (:parent #62))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #54))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("Download one database from\n" 0 27 (:parent #55))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #51]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #56))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #57))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #51] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #59))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("and\n" 0 4 (:parent #62))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #64))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #66))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("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 #67))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("Note for the plant database you can rename it to db" 0 51 (:parent #68)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #68] :use-brackets-p nil) #("webqtl" 0 6 (:parent #72))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #68] :use-brackets-p nil) #("s" 0 1 (:parent #73))) #(", or\nchange the settings in etc/default" 0 39 (:parent #68)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #68] :use-brackets-p nil) #("settings.py" 0 11 (:parent #75))) #("to match your path.\n" 0 20 (:parent #68)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #45]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #51)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #51] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #51))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #48] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #46]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #52))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #49] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #47]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("See " 0 4 (:parent #53)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #53))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #48]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #54)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #54))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #49))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #52))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #52]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #55]) #("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 #58)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("PATH" 0 4 (:parent #62))) #("and R" 0 5 (:parent #58)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("LIBS" 0 4 (:parent #64))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #58] :use-brackets-p nil) #("SITE" 0 4 (:parent #65))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #58))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #55] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #55]) #("On one system:\n" 0 15 (:parent #60))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #55] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #55]) #("and perhaps a few more.\n" 0 24 (:parent #62))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #53)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("data" 0 4 (:parent #65))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #53)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #53] :use-brackets-p nil) #("files" 0 5 (:parent #67))) #("/genotype'" 0 10 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #53]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #56]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #59)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("data" 0 4 (:parent #63))) #(". 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 #59)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("settings.py" 0 11 (:parent #65))) #("(see above in\nthis document).\n" 0 30 (:parent #59))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("You can use the GENENETWORK" 0 27 (:parent #60)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("FILES" 0 5 (:parent #64))) #("switch to set the datadir, for example\n" 0 39 (:parent #60))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #54]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #57]) #("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 #60))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #55]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #58]) #("This error\n" 0 11 (:parent #61))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #58] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("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 #63))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #64)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("LIBS" 0 4 (:parent #68))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #64] :use-brackets-p nil) #("SITE" 0 4 (:parent #69))) #(". 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 #64))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #49] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #56))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #56]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #59]) #("The following error\n" 0 20 (:parent #62))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #59] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #59]) #("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 #64))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #59] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #59]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #66))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #59] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #59]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #68)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #68] :use-brackets-p nil) #("URI" 0 3 (:parent #72))) #("to something like\n" 0 18 (:parent #68))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #59] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #50))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #53]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #56]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #59))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #56] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil 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 #44)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #50))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #44))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #45)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #49))) #("and " 0 4 (:parent #45)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #51))) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #46)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #50))) #(".\n" 0 2 (:parent #46))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #39]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #45))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #47)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #53))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("PATH" 0 4 (:parent #54))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #47))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #44] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("It should upgrade (ignore the locales warnings). 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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 #55)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #59))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #55)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #55] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #55))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #56))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #44] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #44]) #("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 #58))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #42))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #42]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #45]) #("Check out the source with git:\n" 0 31 (:parent #48))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #50))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #45] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #52))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #53))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #54))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #45]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #55))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("And browse on your local machine to " 0 36 (:parent #56)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #56))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #43]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #49)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #49] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #53))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #49))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #44]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #50))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #33] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #48))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #48]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("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 #54))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("As root configure the Guix profile\n" 0 35 (:parent #55))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #51] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("and run for example\n" 0 20 (:parent #57))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #51] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("If you want to run as root you may have to set\n" 0 47 (:parent #59))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("You also need to set\n" 0 21 (:parent #61))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #63))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #64))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #66))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("When you get errors like:\n" 0 26 (:parent #68))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #51]) #("you may need to set\n" 0 20 (:parent #70))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #51] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #45] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #49]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("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 #55)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("webqtl" 0 6 (:parent #59))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("s" 0 1 (:parent #60))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #55)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("webqtl" 0 6 (:parent #62))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("plant" 0 5 (:parent #63))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #55))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("Download one database from\n" 0 27 (:parent #56))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #52]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #57))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #58))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #52] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #60))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("and\n" 0 4 (:parent #63))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #65))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #67))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("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 #68))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("Note for the plant database you can rename it to db" 0 51 (:parent #69)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #69] :use-brackets-p nil) #("webqtl" 0 6 (:parent #73))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #69] :use-brackets-p nil) #("s" 0 1 (:parent #74))) #(", or\nchange the settings in etc/default" 0 39 (:parent #69)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #69] :use-brackets-p nil) #("settings.py" 0 11 (:parent #76))) #("to match your path.\n" 0 20 (:parent #69)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #46]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #49]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #52)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #52] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #52))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #49] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #47]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #53))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #50] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #54))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #48]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("See " 0 4 (:parent #54)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #54] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #54))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #49))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #49]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #55)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #55))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #50))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #53))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #53]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #56]) #("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 #59)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("PATH" 0 4 (:parent #63))) #("and R" 0 5 (:parent #59)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("LIBS" 0 4 (:parent #65))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #59] :use-brackets-p nil) #("SITE" 0 4 (:parent #66))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #59))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #56] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #56]) #("On one system:\n" 0 15 (:parent #61))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #56] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("and perhaps a few more.\n" 0 24 (:parent #63))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #54)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("data" 0 4 (:parent #66))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #54)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #54] :use-brackets-p nil) #("files" 0 5 (:parent #68))) #("/genotype'" 0 10 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #54]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #60)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("data" 0 4 (:parent #64))) #(". 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 #60)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("settings.py" 0 11 (:parent #66))) #("(see above in\nthis document).\n" 0 30 (:parent #60))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("You can use the GENENETWORK" 0 27 (:parent #61)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("FILES" 0 5 (:parent #65))) #("switch to set the datadir, for example\n" 0 39 (:parent #61))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #55]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #58]) #("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 #61))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #56))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #56]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #59]) #("This error\n" 0 11 (:parent #62))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #59] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #59]) #("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 #64))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #59]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #65)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("LIBS" 0 4 (:parent #69))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #65] :use-brackets-p nil) #("SITE" 0 4 (:parent #70))) #(". 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 #65))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #50] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #57))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #57]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #60]) #("The following error\n" 0 20 (:parent #63))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #60] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #60]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #60] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #51))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #51] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 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 #45)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #51))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #45))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #48)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #54))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #48] :use-brackets-p nil) #("PATH" 0 4 (:parent #55))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #48))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #45] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("It should upgrade (ignore the locales warnings). 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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 #56)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #60))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #56)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #56] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #56] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #56))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #57))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #45] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #45]) #("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 #59))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #43))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #43]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #46]) #("Check out the source with git:\n" 0 31 (:parent #49))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #46] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #51))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #46] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("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 #53))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #54))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #55))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #46]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #56))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #46]) #("And browse on your local machine to " 0 36 (:parent #57)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #57] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #57))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #44))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #44]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #47]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #50)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #50] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #54))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #50))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #45))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #45]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #48]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #51))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #34] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #46))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #49))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #49]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("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 #55))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("As root configure the Guix profile\n" 0 35 (:parent #56))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #52] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("and run for example\n" 0 20 (:parent #58))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #52] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("If you want to run as root you may have to set\n" 0 47 (:parent #60))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("You also need to set\n" 0 21 (:parent #62))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #64))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #65))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #67))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("When you get errors like:\n" 0 26 (:parent #69))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #52]) #("you may need to set\n" 0 20 (:parent #71))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #52] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #46] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #50))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #50]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("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 #56)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("webqtl" 0 6 (:parent #60))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("s" 0 1 (:parent #61))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #56)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("webqtl" 0 6 (:parent #63))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #56] :use-brackets-p nil) #("plant" 0 5 (:parent #64))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #56))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("Download one database from\n" 0 27 (:parent #57))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #53]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #58] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #58))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #59))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #53] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #61))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("and\n" 0 4 (:parent #64))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #66))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #53] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #68))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("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 #69))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #53]) #("Note for the plant database you can rename it to db" 0 51 (:parent #70)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #70] :use-brackets-p nil) #("webqtl" 0 6 (:parent #74))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #70] :use-brackets-p nil) #("s" 0 1 (:parent #75))) #(", or\nchange the settings in etc/default" 0 39 (:parent #70)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #70] :use-brackets-p nil) #("settings.py" 0 11 (:parent #77))) #("to match your path.\n" 0 20 (:parent #70)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #47))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #47]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #50]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #53)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #53] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #53))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #50] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #48))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #48]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #51]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #54))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #51] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #55))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #49))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #49]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #52]) #("See " 0 4 (:parent #55)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #55))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #50))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #50]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #53]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #56)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #56] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #56))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #51))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #51] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #54))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #54]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #57]) #("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 #60)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("PATH" 0 4 (:parent #64))) #("and R" 0 5 (:parent #60)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("LIBS" 0 4 (:parent #66))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #60] :use-brackets-p nil) #("SITE" 0 4 (:parent #67))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #60))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #57] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #57]) #("On one system:\n" 0 15 (:parent #62))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #57] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("and perhaps a few more.\n" 0 24 (:parent #64))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #51] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #55)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("data" 0 4 (:parent #67))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #55)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #55] :use-brackets-p nil) #("files" 0 5 (:parent #69))) #("/genotype'" 0 10 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #55]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #58]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #61)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("data" 0 4 (:parent #65))) #(". 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 #61)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #61] :use-brackets-p nil) #("settings.py" 0 11 (:parent #67))) #("(see above in\nthis document).\n" 0 30 (:parent #61))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #58]) #("You can use the GENENETWORK" 0 27 (:parent #62)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #62] :use-brackets-p nil) #("FILES" 0 5 (:parent #66))) #("switch to set the datadir, for example\n" 0 39 (:parent #62))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #58] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #51] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #56))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #56]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #59]) #("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 #62))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #51] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #57))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #57]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #60]) #("This error\n" 0 11 (:parent #63))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #60] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #60]) #("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 #65))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #60]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #66)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("LIBS" 0 4 (:parent #70))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #66] :use-brackets-p nil) #("SITE" 0 4 (:parent #71))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. 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nil nil #61] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #52))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #52] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #55))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 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 #26)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #32))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #26))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("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 #27)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #31))) #("and " 0 4 (:parent #27)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #33))) #(".\n" 0 2 (:parent #27))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #28)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #32))) #(".\n" 0 2 (:parent #28))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #21]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #27))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((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)) #24] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #31]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #34)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #32]) #("A path to the (static) genotype files\n" 0 38 (:parent #35)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #33]) #("Gn-proxy for authentication\n" 0 28 (:parent #36)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2530 2530 2530 2555 2555 0 nil nil nil nil nil nil nil nil # nil nil #34]) #("The genenetwork3 service\n" 0 25 (:parent #37)))) (item (:standard-properties [2555 2555 2562 2568 2568 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2562 2562 2562 2568 2568 0 nil nil nil nil nil nil nil nil # nil nil #35]) #("Redis\n" 0 6 (:parent #38)))) (item (:standard-properties [2568 2568 2575 2583 2583 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #28] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2575 2575 2575 2583 2583 0 nil nil nil nil nil nil nil nil # nil nil #36]) #("Mariadb\n" 0 8 (:parent #39))))))) (headline (:standard-properties [2584 2584 2612 2909 2909 0 (:title) nil nil nil nil 2614 2907 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 26) t] :title (#("Installing Guix packages" 0 24 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2612 2612 2612 2909 2909 0 nil section nil nil nil 2612 2909 nil # nil nil #22]) (paragraph (:standard-properties [2612 2612 2612 2884 2885 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #28)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #28] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #28))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #25] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #23]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #29)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #33))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #29)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #35))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #29] :use-brackets-p nil) #("PATH" 0 4 (:parent #36))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #29))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #31))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #33))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #26] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #35))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #26] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #37)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #41))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #37)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #37))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #38))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #26] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #40))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #24]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Check out the source with git:\n" 0 31 (:parent #30))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #32))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #27] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #34))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #35))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #36))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #37))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("And browse on your local machine to " 0 36 (:parent #38)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #38))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #25]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #31)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #35))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #31))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #26]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #32))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #15] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #30]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("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 #36))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("As root configure the Guix profile\n" 0 35 (:parent #37))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #33] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("and run for example\n" 0 20 (:parent #39))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #33] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you want to run as root you may have to set\n" 0 47 (:parent #41))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("You also need to set\n" 0 21 (:parent #43))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #45))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #46))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #48))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("When you get errors like:\n" 0 26 (:parent #50))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("you may need to set\n" 0 20 (:parent #52))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #31]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("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 #37)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("webqtl" 0 6 (:parent #41))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("s" 0 1 (:parent #42))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #37)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("webqtl" 0 6 (:parent #44))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("plant" 0 5 (:parent #45))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #37))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Download one database from\n" 0 27 (:parent #38))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #34]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #40))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #34] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #42))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("and\n" 0 4 (:parent #45))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #47))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #49))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #50))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Note for the plant database you can rename it to db" 0 51 (:parent #51)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("webqtl" 0 6 (:parent #55))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("s" 0 1 (:parent #56))) #(", or\nchange the settings in etc/default" 0 39 (:parent #51)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("to match your path.\n" 0 20 (:parent #51)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #28]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #34)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #34))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #31] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #29]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #35))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #32] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #36))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #30]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("See " 0 4 (:parent #36)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #36))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #31]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #37)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #37))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #35]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("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 #41)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PATH" 0 4 (:parent #45))) #("and R" 0 5 (:parent #41)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("LIBS" 0 4 (:parent #47))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("SITE" 0 4 (:parent #48))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #41))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("On one system:\n" 0 15 (:parent #43))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #38] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("and perhaps a few more.\n" 0 24 (:parent #45))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #36)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("data" 0 4 (:parent #48))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #36)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("files" 0 5 (:parent #50))) #("/genotype'" 0 10 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #36]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #42)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #46))) #(". 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 #42)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48))) #("(see above in\nthis document).\n" 0 30 (:parent #42))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You can use the GENENETWORK" 0 27 (:parent #43)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("FILES" 0 5 (:parent #47))) #("switch to set the datadir, for example\n" 0 39 (:parent #43))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #37]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #40]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #47))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #39]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("The following error\n" 0 20 (:parent #45))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #42] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #42] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #36]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #42))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #43] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12428 12428 12428 12441 12441 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("Base install\n" 0 13 (:parent #49))) (plain-list (:standard-properties [12441 12441 12441 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #46] :type unordered) (item (:standard-properties [12441 12441 12449 12502 12502 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12449 12449 12449 12502 12502 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #56)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("Get Guix build going\n" 0 21 (:parent #57))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #58] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12541 12541 12541 12575 12575 0 nil nil nil nil nil nil nil nil # nil nil #61]) #("Build the correct version of Guix\n" 0 34 (:parent #64)))) (item (:standard-properties [12575 12575 12585 12702 12702 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #58] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12585 12585 12585 12702 12702 0 nil nil nil nil nil nil nil nil # nil nil #62]) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #65)) (link (:standard-properties [12648 nil nil nil 12701 0 nil nil nil nil nil nil nil nil # nil nil #65] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #65)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #58] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # nil nil #63]) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #66)))))) (item (:standard-properties [12780 12780 12788 12826 12826 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12788 12788 12788 12826 12826 0 nil nil nil nil nil nil nil nil # nil nil #55]) #("Create a gn2 user and home with space\n" 0 38 (:parent #58)))) (item (:standard-properties [12826 12826 12834 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12834 12834 12834 12848 12848 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("Install redis\n" 0 14 (:parent #59))) (plain-list (:standard-properties [12848 12848 12848 12926 12926 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #56] :type unordered) (item (:standard-properties [12848 12848 12858 12873 12873 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12858 12858 12858 12873 12873 0 nil nil nil nil nil nil nil nil # nil nil #63]) #("add to systemd\n" 0 15 (:parent #66)))) (item (:standard-properties [12873 12873 12883 12900 12900 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12883 12883 12883 12900 12900 0 nil nil nil nil nil nil nil nil # nil nil #64]) #("update redis.cnf\n" 0 17 (:parent #67)))) (item (:standard-properties [12900 12900 12910 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #60] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12910 12910 12910 12926 12926 0 nil nil nil nil nil nil nil nil # nil nil #65]) #("update database\n" 0 16 (:parent #68)))))) (item (:standard-properties [12926 12926 12934 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12934 12934 12934 12984 12984 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #60))) (plain-list (:standard-properties [12984 12984 12984 13151 13151 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #57] :type unordered) (item (:standard-properties [12984 12984 12994 13009 13009 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #61] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12994 12994 12994 13009 13009 0 nil nil nil nil nil nil nil nil # nil nil #64]) #("add to systemd\n" 0 15 (:parent #67)))) (item (:standard-properties [13009 13009 13019 13037 13037 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #61] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13019 13019 13019 13037 13037 0 nil nil nil nil nil nil nil nil # nil nil #65]) #("system stop mysql\n" 0 18 (:parent #68)))) (item (:standard-properties [13037 13037 13047 13064 13064 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "[ ]" 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((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)) #353] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #360]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #363)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #361]) #("A path to the (static) genotype files\n" 0 38 (:parent #364)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #357] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #362]) #("Gn-proxy for authentication\n" 0 28 (:parent #365)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((2390 0 "1. 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Follow the instructions on\n" 0 117 (:parent #357)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #357))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #352]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #355]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #358)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #358] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #362))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #360))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #362))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #364))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #355] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #356] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #359))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #359]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("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 #365))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("As root configure the Guix profile\n" 0 35 (:parent #366))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #362] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("and run for example\n" 0 20 (:parent #368))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #362] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("If you want to run as root you may have to set\n" 0 47 (:parent #370))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("You also need to set\n" 0 21 (:parent #372))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #374))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #375))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #377))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("When you get errors like:\n" 0 26 (:parent #379))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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You can find them in\n" 0 58 (:parent #363)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #363] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #363))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #360] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #358]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #364))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #361] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #359))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #359]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("See " 0 4 (:parent #365)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #365))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #360))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #360]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #366)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #382]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #385)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #379] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #383]) #("Get Guix build going\n" 0 21 (:parent #386))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #383] :type unordered) (item (:standard-properties [12531 12531 12541 12575 12575 0 (:tag) item nil nil nil nil nil nil # 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nil nil #394] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #394)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #387] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #33))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #26] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #35))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #26] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #37)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #41))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #37)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #37))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #38))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #26] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("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 #40))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #24]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Check out the source with git:\n" 0 31 (:parent #30))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #32))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #27] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #34))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #35))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #36))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #27]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #37))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("And browse on your local machine to " 0 36 (:parent #38)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #38))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #25]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #31)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #35))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #31))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #26]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #32))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #15] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #30]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("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 #36))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("As root configure the Guix profile\n" 0 35 (:parent #37))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #33] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("and run for example\n" 0 20 (:parent #39))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #33] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("If you want to run as root you may have to set\n" 0 47 (:parent #41))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("You also need to set\n" 0 21 (:parent #43))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #45))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #46))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #48))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("When you get errors like:\n" 0 26 (:parent #50))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("you may need to set\n" 0 20 (:parent #52))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #31]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("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 #37)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("webqtl" 0 6 (:parent #41))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("s" 0 1 (:parent #42))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #37)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("webqtl" 0 6 (:parent #44))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("plant" 0 5 (:parent #45))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #37))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Download one database from\n" 0 27 (:parent #38))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #34]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #40))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #34] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #42))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("and\n" 0 4 (:parent #45))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #47))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #49))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("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 #50))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Note for the plant database you can rename it to db" 0 51 (:parent #51)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("webqtl" 0 6 (:parent #55))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("s" 0 1 (:parent #56))) #(", or\nchange the settings in etc/default" 0 39 (:parent #51)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("settings.py" 0 11 (:parent #58))) #("to match your path.\n" 0 20 (:parent #51)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #28]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #34)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #34))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #31] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #29]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #35))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #32] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #36))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #30]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("See " 0 4 (:parent #36)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #36] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #36))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #31]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #37)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #37))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #35]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("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 #41)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("PATH" 0 4 (:parent #45))) #("and R" 0 5 (:parent #41)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("LIBS" 0 4 (:parent #47))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("SITE" 0 4 (:parent #48))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #41))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #38] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("On one system:\n" 0 15 (:parent #43))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #38] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #38]) #("and perhaps a few more.\n" 0 24 (:parent #45))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #36)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("data" 0 4 (:parent #48))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #36)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("files" 0 5 (:parent #50))) #("/genotype'" 0 10 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #36]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #42)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("data" 0 4 (:parent #46))) #(". 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 #42)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48))) #("(see above in\nthis document).\n" 0 30 (:parent #42))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("You can use the GENENETWORK" 0 27 (:parent #43)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("FILES" 0 5 (:parent #47))) #("switch to set the datadir, for example\n" 0 39 (:parent #43))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #37]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #40]) #("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 #43))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #38]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("This error\n" 0 11 (:parent #44))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("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 #46))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #47)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("LIBS" 0 4 (:parent #51))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #47] :use-brackets-p nil) #("SITE" 0 4 (:parent #52))) #(". 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 #47))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #32] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #39))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #39]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #42]) #("The following error\n" 0 20 (:parent #45))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #42] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("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 #47))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #49))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #42]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #51)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("URI" 0 3 (:parent #55))) #("to something like\n" 0 18 (:parent #51))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #42] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #36]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #42))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #39] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #30)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #36))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("PATH" 0 4 (:parent #37))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #30))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #32))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #27] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #34))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #27] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #36))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #27] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #38)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #42))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #38)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #38))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #39))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #27] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("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 #41))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #25]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Check out the source with git:\n" 0 31 (:parent #31))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #33))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #28] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("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 #35))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #36))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #37))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #28]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #38))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("And browse on your local machine to " 0 36 (:parent #39)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #39] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #39))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #26]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #32)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #36))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #32))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #27]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #33))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #16] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #31]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("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 #37))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("As root configure the Guix profile\n" 0 35 (:parent #38))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #34] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("and run for example\n" 0 20 (:parent #40))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #34] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("If you want to run as root you may have to set\n" 0 47 (:parent #42))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("You also need to set\n" 0 21 (:parent #44))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #46))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #47))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #49))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("When you get errors like:\n" 0 26 (:parent #51))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("you may need to set\n" 0 20 (:parent #53))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #32]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("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 #38)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("webqtl" 0 6 (:parent #42))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("s" 0 1 (:parent #43))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #38)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("webqtl" 0 6 (:parent #45))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("plant" 0 5 (:parent #46))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #38))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Download one database from\n" 0 27 (:parent #39))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #35]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #40] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #40))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #41))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #35] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #43))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("and\n" 0 4 (:parent #46))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #48))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #50))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("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 #51))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("Note for the plant database you can rename it to db" 0 51 (:parent #52)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("webqtl" 0 6 (:parent #56))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("s" 0 1 (:parent #57))) #(", or\nchange the settings in etc/default" 0 39 (:parent #52)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("settings.py" 0 11 (:parent #59))) #("to match your path.\n" 0 20 (:parent #52)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #29]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #35)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #35] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #35))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #32] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #30))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #30]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #36))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #33] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #37))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #31))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #31]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("See " 0 4 (:parent #37)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #37] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #37))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #32))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #32]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #35]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #38)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #38] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #38))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #33))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #36))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #36]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("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 #42)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("PATH" 0 4 (:parent #46))) #("and R" 0 5 (:parent #42)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("LIBS" 0 4 (:parent #48))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("SITE" 0 4 (:parent #49))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #42))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #39] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #39]) #("On one system:\n" 0 15 (:parent #44))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #39] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #39]) #("and perhaps a few more.\n" 0 24 (:parent #46))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #37)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("data" 0 4 (:parent #49))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #37)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("files" 0 5 (:parent #51))) #("/genotype'" 0 10 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #37]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #43)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("data" 0 4 (:parent #47))) #(". 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 #43)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #43] :use-brackets-p nil) #("settings.py" 0 11 (:parent #49))) #("(see above in\nthis document).\n" 0 30 (:parent #43))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("You can use the GENENETWORK" 0 27 (:parent #44)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #44] :use-brackets-p nil) #("FILES" 0 5 (:parent #48))) #("switch to set the datadir, for example\n" 0 39 (:parent #44))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #38))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #38]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #41]) #("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. 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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 #48))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #33] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #40))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #40]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #43]) #("The following error\n" 0 20 (:parent #46))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #43] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #43]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #43] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #34))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #34] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #37))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #37]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #43))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #24)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #30))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("PATH" 0 4 (:parent #31))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #24))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #26))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #28))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #21] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #30))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #21] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #32)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #36))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #32)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #32))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #33))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #21] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #35))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #19]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Check out the source with git:\n" 0 31 (:parent #25))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #22] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #27))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #22] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #29))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #30))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #31))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #32))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("And browse on your local machine to " 0 36 (:parent #33)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #33))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #20]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #26)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #30))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #26))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #21]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #27))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #10] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #25]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("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 #31))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("As root configure the Guix profile\n" 0 35 (:parent #32))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #28] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("and run for example\n" 0 20 (:parent #34))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #28] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you want to run as root you may have to set\n" 0 47 (:parent #36))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("You also need to set\n" 0 21 (:parent #38))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #40))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #41))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #43))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("When you get errors like:\n" 0 26 (:parent #45))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("you may need to set\n" 0 20 (:parent #47))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #26]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("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 #32)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("webqtl" 0 6 (:parent #36))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("s" 0 1 (:parent #37))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #32)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("webqtl" 0 6 (:parent #39))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("plant" 0 5 (:parent #40))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #32))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Download one database from\n" 0 27 (:parent #33))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #29]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #34))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #35))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #29] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #37))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("and\n" 0 4 (:parent #40))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #42))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #44))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("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 #45))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Note for the plant database you can rename it to db" 0 51 (:parent #46)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("webqtl" 0 6 (:parent #50))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("s" 0 1 (:parent #51))) #(", or\nchange the settings in etc/default" 0 39 (:parent #46)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("settings.py" 0 11 (:parent #53))) #("to match your path.\n" 0 20 (:parent #46)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #23]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #29)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #29))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #26] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #24]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #30))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #27] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #31))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #25]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("See " 0 4 (:parent #31)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #31))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #26]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #32)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #32))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #30]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("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 #36)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("PATH" 0 4 (:parent #40))) #("and R" 0 5 (:parent #36)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("LIBS" 0 4 (:parent #42))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("SITE" 0 4 (:parent #43))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #36))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("On one system:\n" 0 15 (:parent #38))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #33] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #33]) #("and perhaps a few more.\n" 0 24 (:parent #40))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #31)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("data" 0 4 (:parent #43))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #31)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("files" 0 5 (:parent #45))) #("/genotype'" 0 10 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #31]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #37)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("data" 0 4 (:parent #41))) #(". 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 #37)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("settings.py" 0 11 (:parent #43))) #("(see above in\nthis document).\n" 0 30 (:parent #37))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("You can use the GENENETWORK" 0 27 (:parent #38)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("FILES" 0 5 (:parent #42))) #("switch to set the datadir, for example\n" 0 39 (:parent #38))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #32]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #35]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #42))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #34]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("The following error\n" 0 20 (:parent #40))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #37] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #37] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #31]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #37))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #38] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12428 12428 12428 12441 12441 0 nil nil nil nil nil nil nil nil # nil nil #41]) #("Base install\n" 0 13 (:parent #44))) (plain-list (:standard-properties [12441 12441 12441 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #41] :type unordered) (item (:standard-properties [12441 12441 12449 12502 12502 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12449 12449 12449 12502 12502 0 nil nil nil nil nil nil nil nil # nil nil #48]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #51)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #49]) #("Get Guix build going\n" 0 21 (:parent #52))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #53] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12541 12541 12541 12575 12575 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("Build the correct version of Guix\n" 0 34 (:parent #59)))) (item (:standard-properties [12575 12575 12585 12702 12702 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #53] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12585 12585 12585 12702 12702 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #60)) (link (:standard-properties [12648 nil nil nil 12701 0 nil nil nil nil nil nil nil nil # nil nil #60] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #60)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #53] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # nil nil #58]) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #61)))))) (item (:standard-properties [12780 12780 12788 12826 12826 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12788 12788 12788 12826 12826 0 nil nil nil nil nil nil nil nil # nil nil #50]) #("Create a gn2 user and home with space\n" 0 38 (:parent #53)))) (item (:standard-properties [12826 12826 12834 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12834 12834 12834 12848 12848 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("Install redis\n" 0 14 (:parent #54))) (plain-list (:standard-properties [12848 12848 12848 12926 12926 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :type unordered) (item (:standard-properties [12848 12848 12858 12873 12873 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12858 12858 12858 12873 12873 0 nil nil nil nil nil nil nil nil # nil nil #58]) #("add to systemd\n" 0 15 (:parent #61)))) (item (:standard-properties [12873 12873 12883 12900 12900 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12883 12883 12883 12900 12900 0 nil nil nil nil nil nil nil nil # nil nil #59]) #("update redis.cnf\n" 0 17 (:parent #62)))) (item (:standard-properties [12900 12900 12910 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #55] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12910 12910 12910 12926 12926 0 nil nil nil nil nil nil nil nil # nil nil #60]) #("update database\n" 0 16 (:parent #63)))))) (item (:standard-properties [12926 12926 12934 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #45] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12934 12934 12934 12984 12984 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #55))) (plain-list (:standard-properties [12984 12984 12984 13151 13151 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #52] :type unordered) (item (:standard-properties [12984 12984 12994 13009 13009 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #56] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12994 12994 12994 13009 13009 0 nil nil nil nil nil nil nil nil # nil nil #59]) #("add to systemd\n" 0 15 (:parent #62)))) (item (:standard-properties [13009 13009 13019 13037 13037 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #56] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13019 13019 13019 13037 13037 0 nil nil nil nil nil nil nil nil # nil nil #60]) #("system stop mysql\n" 0 18 (:parent #63)))) (item (:standard-properties [13037 13037 13047 13064 13064 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "[ ]" 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). 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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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #376))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #378))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #380)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("URI" 0 3 (:parent #384))) #("to something like\n" 0 18 (:parent #380))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #24)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #30))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #24] :use-brackets-p nil) #("PATH" 0 4 (:parent #31))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #24))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #26))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #21] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #28))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #21] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #30))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #21] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #32)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #36))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #32)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #32))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #33))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #21] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #21]) #("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 #35))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #19]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Check out the source with git:\n" 0 31 (:parent #25))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #22] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #27))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #22] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #29))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #30))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #31))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #22]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #32))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("And browse on your local machine to " 0 36 (:parent #33)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #33))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #20]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #26)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #30))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #26))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #21]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #27))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #10] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #25]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("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 #31))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("As root configure the Guix profile\n" 0 35 (:parent #32))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #28] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("and run for example\n" 0 20 (:parent #34))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #28] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("If you want to run as root you may have to set\n" 0 47 (:parent #36))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("You also need to set\n" 0 21 (:parent #38))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #40))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #41))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #43))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("When you get errors like:\n" 0 26 (:parent #45))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("you may need to set\n" 0 20 (:parent #47))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #26]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("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 #32)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("webqtl" 0 6 (:parent #36))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("s" 0 1 (:parent #37))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #32)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("webqtl" 0 6 (:parent #39))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("plant" 0 5 (:parent #40))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #32))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Download one database from\n" 0 27 (:parent #33))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #29]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #34))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #35))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #29] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #37))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("and\n" 0 4 (:parent #40))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #42))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #44))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("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 #45))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Note for the plant database you can rename it to db" 0 51 (:parent #46)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("webqtl" 0 6 (:parent #50))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("s" 0 1 (:parent #51))) #(", or\nchange the settings in etc/default" 0 39 (:parent #46)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("settings.py" 0 11 (:parent #53))) #("to match your path.\n" 0 20 (:parent #46)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #23]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #29)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #29))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #26] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #24))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #24]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #30))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #27] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #31))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #25]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("See " 0 4 (:parent #31)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #31] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #31))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #26]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #32)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #32))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #30))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #30]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #33]) #("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 #36)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("PATH" 0 4 (:parent #40))) #("and R" 0 5 (:parent #36)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("LIBS" 0 4 (:parent #42))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("SITE" 0 4 (:parent #43))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #36))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #33] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #33]) #("On one system:\n" 0 15 (:parent #38))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #33] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #33]) #("and perhaps a few more.\n" 0 24 (:parent #40))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #31)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("data" 0 4 (:parent #43))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #31)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("files" 0 5 (:parent #45))) #("/genotype'" 0 10 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #31]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #37)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("data" 0 4 (:parent #41))) #(". 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 #37)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("settings.py" 0 11 (:parent #43))) #("(see above in\nthis document).\n" 0 30 (:parent #37))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #34]) #("You can use the GENENETWORK" 0 27 (:parent #38)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("FILES" 0 5 (:parent #42))) #("switch to set the datadir, for example\n" 0 39 (:parent #38))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #34] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #32]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #35]) #("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 #38))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #33]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #36]) #("This error\n" 0 11 (:parent #39))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #36] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("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 #41))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #36]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #42)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("LIBS" 0 4 (:parent #46))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #42] :use-brackets-p nil) #("SITE" 0 4 (:parent #47))) #(". 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 #42))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #27] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #34))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #34]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #37]) #("The following error\n" 0 20 (:parent #40))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #37] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("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 #42))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #44))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #37]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #46)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #46] :use-brackets-p nil) #("URI" 0 3 (:parent #50))) #("to something like\n" 0 18 (:parent #46))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #37] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # 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Follow the instructions on\n" 0 117 (:parent #24)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #24] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #25)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #31))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("PATH" 0 4 (:parent #32))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #25))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #22] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("It should upgrade (ignore the locales warnings). 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #29))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #22] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #31))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #22] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #33)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #37))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #33)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #33] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #33] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #33))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #34))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #22] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("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 #36))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #20]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("Check out the source with git:\n" 0 31 (:parent #26))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #28))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #23] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("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 #30))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #31))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #32))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #23]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #33))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("And browse on your local machine to " 0 36 (:parent #34)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #34] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #34))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #21]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #27)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #31))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #27))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #22]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #28))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #11] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #26]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("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 #32))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("As root configure the Guix profile\n" 0 35 (:parent #33))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #29] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("and run for example\n" 0 20 (:parent #35))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #29] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("If you want to run as root you may have to set\n" 0 47 (:parent #37))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("You also need to set\n" 0 21 (:parent #39))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #41))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #42))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #44))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("When you get errors like:\n" 0 26 (:parent #46))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # 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You can find them in\n" 0 58 (:parent #30)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #30] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #30))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #27] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #25))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #25]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #31))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #28] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #32))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #26))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #26]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("See " 0 4 (:parent #32)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #32] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #32))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #27))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #27]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #30]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #33)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #33] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #33))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #28))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #31))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #31]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #34]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. 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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 #38)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #38] :use-brackets-p nil) #("settings.py" 0 11 (:parent #44))) #("(see above in\nthis document).\n" 0 30 (:parent #38))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #35]) #("You can use the GENENETWORK" 0 27 (:parent #39)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #39] :use-brackets-p nil) #("FILES" 0 5 (:parent #43))) #("switch to set the datadir, for example\n" 0 39 (:parent #39))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #35] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #33))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #33]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #36]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #43))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #28] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #35))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #35]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("The following error\n" 0 20 (:parent #41))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #38] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #38]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #38] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #11] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #29))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #29] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #32))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 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 #16)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #22))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #16))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #13]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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" 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)) #14] :type ordered) (item (:standard-properties [2390 2390 2397 2443 2443 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2397 2397 2397 2443 2443 0 nil nil nil nil nil nil nil nil # nil nil #21]) #("GNU Guix with a guix profile for genenetwork2\n" 0 46 (:parent #24)))) (item (:standard-properties [2443 2443 2450 2488 2488 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2450 2450 2450 2488 2488 0 nil nil nil nil nil nil nil nil # nil nil #22]) #("A path to the (static) genotype files\n" 0 38 (:parent #25)))) (item (:standard-properties [2488 2488 2495 2523 2523 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2495 2495 2495 2523 2523 0 nil nil nil nil nil nil nil nil # nil nil #23]) #("Gn-proxy for authentication\n" 0 28 (:parent #26)))) (item (:standard-properties [2523 2523 2530 2555 2555 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2530 2530 2530 2555 2555 0 nil nil nil nil nil nil nil nil # nil nil #24]) #("The genenetwork3 service\n" 0 25 (:parent #27)))) (item (:standard-properties [2555 2555 2562 2568 2568 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2562 2562 2562 2568 2568 0 nil nil nil nil nil nil nil nil # nil nil #25]) #("Redis\n" 0 6 (:parent #28)))) (item (:standard-properties [2568 2568 2575 2583 2583 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #18] :bullet "1. " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [2575 2575 2575 2583 2583 0 nil nil nil nil nil nil nil nil # nil nil #26]) #("Mariadb\n" 0 8 (:parent #29))))))) (headline (:standard-properties [2584 2584 2612 2909 2909 0 (:title) nil nil nil nil 2614 2907 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 26) t] :title (#("Installing Guix packages" 0 24 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2612 2612 2612 2909 2909 0 nil section nil nil nil 2612 2909 nil # nil nil #12]) (paragraph (:standard-properties [2612 2612 2612 2884 2885 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #18)) (link (:standard-properties [2729 nil nil nil 2767 1 nil nil nil nil nil nil nil nil # nil nil #18] :type "fuzzy" :type-explicit-p nil :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #18))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #15] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #13))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #13]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #16]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #19)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #19] :type "https" :type-explicit-p t :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) #("guix-bioinformatics" 0 19 (:parent #23))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #19)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #19] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #25))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #19] :use-brackets-p nil) #("PATH" 0 4 (:parent #26))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #19))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #21))) (fixed-width (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #23))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #16] :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=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #25))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #27)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #31))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #27)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #27))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #28))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #16] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #30))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #14]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("Check out the source with git:\n" 0 31 (:parent #20))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #22))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #17] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("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 #24))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #25))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #26))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #17]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #27))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("And browse on your local machine to " 0 36 (:parent #28)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #28))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #15]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #21)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #25))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #21))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #16]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #22))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #5] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #20))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #20]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("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 #26))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("As root configure the Guix profile\n" 0 35 (:parent #27))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #23] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("and run for example\n" 0 20 (:parent #29))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #23] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you want to run as root you may have to set\n" 0 47 (:parent #31))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("You also need to set\n" 0 21 (:parent #33))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #35))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #36))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #38))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("When you get errors like:\n" 0 26 (:parent #40))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("you may need to set\n" 0 20 (:parent #42))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #21]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("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 #27)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("webqtl" 0 6 (:parent #31))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("s" 0 1 (:parent #32))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #27)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("webqtl" 0 6 (:parent #34))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("plant" 0 5 (:parent #35))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #27))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Download one database from\n" 0 27 (:parent #28))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #24]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #29))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #30))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #24] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #32))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("and\n" 0 4 (:parent #35))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #37))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #39))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("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 #40))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Note for the plant database you can rename it to db" 0 51 (:parent #41)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("webqtl" 0 6 (:parent #45))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("s" 0 1 (:parent #46))) #(", or\nchange the settings in etc/default" 0 39 (:parent #41)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48))) #("to match your path.\n" 0 20 (:parent #41)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #18]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #24)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #24))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #21] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #19]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #25))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #22] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #26))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #20]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("See " 0 4 (:parent #26)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #26))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #21]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #27)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #27))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #25]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("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 #31)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("PATH" 0 4 (:parent #35))) #("and R" 0 5 (:parent #31)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("LIBS" 0 4 (:parent #37))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("SITE" 0 4 (:parent #38))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #31))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("On one system:\n" 0 15 (:parent #33))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #28] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #28]) #("and perhaps a few more.\n" 0 24 (:parent #35))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #26)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("data" 0 4 (:parent #38))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #26)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("files" 0 5 (:parent #40))) #("/genotype'" 0 10 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #26]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #32)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("data" 0 4 (:parent #36))) #(". 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 #32)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("settings.py" 0 11 (:parent #38))) #("(see above in\nthis document).\n" 0 30 (:parent #32))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("You can use the GENENETWORK" 0 27 (:parent #33)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("FILES" 0 5 (:parent #37))) #("switch to set the datadir, for example\n" 0 39 (:parent #33))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #27]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #30]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #37))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #29))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #29]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("The following error\n" 0 20 (:parent #35))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #32] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #32] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #26]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #32))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #33] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12428 12428 12428 12441 12441 0 nil nil nil nil nil nil nil nil # nil nil #36]) #("Base install\n" 0 13 (:parent #39))) (plain-list (:standard-properties [12441 12441 12441 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #36] :type unordered) (item (:standard-properties [12441 12441 12449 12502 12502 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12449 12449 12449 12502 12502 0 nil nil nil nil nil nil nil nil # nil nil #43]) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #46)))) (item (:standard-properties [12502 12502 12510 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12510 12510 12510 12531 12531 0 nil nil nil nil nil nil nil nil # nil nil #44]) #("Get Guix build going\n" 0 21 (:parent #47))) (plain-list (:standard-properties [12531 12531 12531 12780 12780 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 "- 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"+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) #48] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12541 12541 12541 12575 12575 0 nil nil nil nil nil nil nil nil # nil nil #51]) #("Build the correct version of Guix\n" 0 34 (:parent #54)))) (item (:standard-properties [12575 12575 12585 12702 12702 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #48] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12585 12585 12585 12702 12702 0 nil nil nil nil nil nil nil nil # nil nil #52]) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #55)) (link (:standard-properties [12648 nil nil nil 12701 0 nil nil nil nil nil nil nil nil # nil nil #55] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #55)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #48] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #56)))))) (item (:standard-properties [12780 12780 12788 12826 12826 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12788 12788 12788 12826 12826 0 nil nil nil nil nil nil nil nil # nil nil #45]) #("Create a gn2 user and home with space\n" 0 38 (:parent #48)))) (item (:standard-properties [12826 12826 12834 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12834 12834 12834 12848 12848 0 nil nil nil nil nil nil nil nil # nil nil #46]) #("Install redis\n" 0 14 (:parent #49))) (plain-list (:standard-properties [12848 12848 12848 12926 12926 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #46] :type unordered) (item (:standard-properties [12848 12848 12858 12873 12873 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12858 12858 12858 12873 12873 0 nil nil nil nil nil nil nil nil # nil nil #53]) #("add to systemd\n" 0 15 (:parent #56)))) (item (:standard-properties [12873 12873 12883 12900 12900 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12883 12883 12883 12900 12900 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("update redis.cnf\n" 0 17 (:parent #57)))) (item (:standard-properties [12900 12900 12910 12926 12926 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #50] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12910 12910 12910 12926 12926 0 nil nil nil nil nil nil nil nil # nil nil #55]) #("update database\n" 0 16 (:parent #58)))))) (item (:standard-properties [12926 12926 12934 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #40] :bullet "+ " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12934 12934 12934 12984 12984 0 nil nil nil nil nil nil nil nil # nil nil #47]) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #50))) (plain-list (:standard-properties [12984 12984 12984 13151 13151 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #47] :type unordered) (item (:standard-properties [12984 12984 12994 13009 13009 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12994 12994 12994 13009 13009 0 nil nil nil nil nil nil nil nil # nil nil #54]) #("add to systemd\n" 0 15 (:parent #57)))) (item (:standard-properties [13009 13009 13019 13037 13037 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13019 13019 13019 13037 13037 0 nil nil nil nil nil nil nil nil # nil nil #55]) #("system stop mysql\n" 0 18 (:parent #58)))) (item (:standard-properties [13037 13037 13047 13064 13064 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13047 13047 13047 13064 13064 0 nil nil nil nil nil nil nil nil # nil nil #56]) #("update mysql.cnf\n" 0 17 (:parent #59)))) (item (:standard-properties [13064 13064 13074 13128 13128 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #51] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13074 13074 13074 13128 13128 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("update database (see gn-services/services/mariadb.md)\n" 0 54 (:parent #60)))) (item (:standard-properties [13128 13128 13138 13151 13151 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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 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"- " 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)) #54] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [13227 13227 13227 13242 13242 0 nil nil nil nil nil nil nil nil # nil nil #57]) #("add to systemd\n" 0 15 (:parent #60)))))))))))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #0))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [121 121 121 1439 1439 0 nil section nil nil nil 121 1439 nil # nil nil #0]) (plain-list (:standard-properties [121 121 121 1438 1439 1 nil planning nil nil nil nil nil nil # nil ((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)) #3] :type unordered) (item (:standard-properties [121 121 124 156 156 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [124 124 124 156 156 0 nil nil nil nil nil nil nil nil # nil nil #9]) (link (:standard-properties [124 nil 141 153 155 0 nil nil nil nil nil nil nil nil # nil nil #12] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:standard-properties [156 156 159 187 187 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [159 159 159 187 187 0 nil nil nil nil nil nil nil nil # nil nil #10]) (link (:standard-properties [159 nil 174 184 186 0 nil nil nil nil nil nil nil nil # nil nil #13] :type "custom-id" :type-explicit-p nil :path "check-list" :format bracket :raw-link "#check-list" :application nil :search-option nil) #("Check list" 0 10 (:parent #16))) #("\n" 0 1 (:parent #13)))) (item (:standard-properties [187 187 190 246 246 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [190 190 190 246 246 0 nil nil nil nil nil nil nil nil # nil nil #11]) (link (:standard-properties [190 nil 219 243 245 0 nil nil nil nil nil nil nil nil # nil nil #14] :type "custom-id" :type-explicit-p nil :path "installing-guix-packages" :format bracket :raw-link "#installing-guix-packages" :application nil :search-option nil) #("Installing Guix packages" 0 24 (:parent #17))) #("\n" 0 1 (:parent #14)))) (item (:standard-properties [246 246 249 311 311 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [249 249 249 311 311 0 nil nil nil nil nil nil nil nil # nil nil #12]) (link (:standard-properties [249 nil 281 308 310 0 nil nil nil nil nil nil nil nil # nil nil #15] :type "custom-id" :type-explicit-p nil :path "creating-a-gnu-guix-profile" :format bracket :raw-link "#creating-a-gnu-guix-profile" :application nil :search-option nil) #("Creating a GNU Guix profile" 0 27 (:parent #18))) #("\n" 0 1 (:parent #15)))) (item (:standard-properties [311 311 314 344 344 0 (:tag) item nil nil nil nil nil nil # nil ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 187) (187 1 "- 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GN2" 0 11 (:parent #19))) #("\n" 0 1 (:parent #16)))) (item (:standard-properties [344 344 347 379 379 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [347 347 347 379 379 0 nil nil nil nil nil nil nil nil # nil nil #14]) (link (:standard-properties [347 nil 364 376 378 0 nil nil nil nil nil nil nil nil # nil nil #17] :type "custom-id" :type-explicit-p nil :path "run-gn-proxy" :format bracket :raw-link "#run-gn-proxy" :application nil :search-option nil) #("Run gn-proxy" 0 12 (:parent #20))) #("\n" 0 1 (:parent #17)))) (item (:standard-properties [379 379 382 408 408 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [382 382 382 408 408 0 nil nil nil nil nil nil nil nil # nil nil #15]) (link (:standard-properties [382 nil 396 405 407 0 nil nil nil nil nil nil nil nil # nil nil #18] :type "custom-id" :type-explicit-p nil :path "run-redis" :format bracket :raw-link "#run-redis" :application nil :search-option nil) #("Run Redis" 0 9 (:parent #21))) #("\n" 0 1 (:parent #18)))) (item (:standard-properties [408 408 411 603 603 0 (:tag) item nil nil nil nil nil nil # nil ((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)) #6] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [411 411 411 455 455 0 nil nil nil nil nil nil nil nil # nil nil #16]) (link (:standard-properties [411 nil 434 452 454 0 nil nil nil nil nil nil nil nil # nil nil #19] :type "custom-id" :type-explicit-p nil :path "run-mariadb-server" :format bracket :raw-link "#run-mariadb-server" :application nil :search-option nil) #("Run MariaDB server" 0 18 (:parent #22))) #("\n" 0 1 (:parent #19))) (plain-list (:standard-properties [455 455 455 603 603 0 nil nil nil nil nil nil nil nil # nil ((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 "- 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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 #355)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #361))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #355))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("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 #356)) (link (:standard-properties [2047 nil 2101 2120 2123 1 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil) #("Guix bioinformatics" 0 19 (:parent #360))) #("and " 0 4 (:parent #356)) (link (:standard-properties [2127 nil 2166 2174 2176 0 nil nil nil nil nil nil nil nil # nil nil #356] :type "https" :type-explicit-p t :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil) #("GNU Guix" 0 8 (:parent #362))) #(".\n" 0 2 (:parent #356))) (paragraph (:standard-properties [2179 2179 2179 2314 2315 1 nil nil nil nil nil nil nil nil # nil nil #352]) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #357)) (link (:standard-properties [2265 nil 2290 2310 2312 0 nil nil nil nil nil nil nil nil # nil nil #357] :type "custom-id" :type-explicit-p nil :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil) #("GN2 Dependency Graph" 0 20 (:parent #361))) #(".\n" 0 2 (:parent #357))))) (headline (:standard-properties [2315 2315 2329 2584 2584 0 (:title) nil nil nil nil 2331 2582 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 12) t] :title (#("Check list" 0 10 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2329 2329 2329 2584 2584 0 nil section nil nil nil 2329 2584 nil # nil nil #350]) (paragraph (:standard-properties [2329 2329 2329 2389 2390 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #356))) (plain-list (:standard-properties [2390 2390 2390 2583 2584 1 nil nil nil nil nil nil nil nil # nil ((2390 0 "1. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #358)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #364))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #358] :use-brackets-p nil) #("PATH" 0 4 (:parent #365))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #358))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("It should upgrade (ignore the locales warnings). 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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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #376))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #378))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #380)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("URI" 0 3 (:parent #384))) #("to something like\n" 0 18 (:parent #380))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #19)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #19] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #25))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #19] :use-brackets-p nil) #("PATH" 0 4 (:parent #26))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #19))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("It should upgrade (ignore the locales warnings). 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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #23))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #16] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #25))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #16] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #27)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #31))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #27)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #27))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #28))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #16] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("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 #30))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #14]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("Check out the source with git:\n" 0 31 (:parent #20))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #22))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #17] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("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 #24))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #25))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #26))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #17]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #27))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("And browse on your local machine to " 0 36 (:parent #28)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #28] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #28))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #15]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #21)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #25))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #21))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #16]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #22))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #5] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #20))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #20]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("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 #26))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("As root configure the Guix profile\n" 0 35 (:parent #27))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #23] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("and run for example\n" 0 20 (:parent #29))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #23] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("If you want to run as root you may have to set\n" 0 47 (:parent #31))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("You also need to set\n" 0 21 (:parent #33))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #35))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #36))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #38))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("When you get errors like:\n" 0 26 (:parent #40))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("you may need to set\n" 0 20 (:parent #42))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #21]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("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 #27)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("webqtl" 0 6 (:parent #31))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("s" 0 1 (:parent #32))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #27)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("webqtl" 0 6 (:parent #34))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("plant" 0 5 (:parent #35))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #27))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Download one database from\n" 0 27 (:parent #28))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #24]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #29] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #29))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #30))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #24] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #32))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("and\n" 0 4 (:parent #35))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #37))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #39))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("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 #40))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("Note for the plant database you can rename it to db" 0 51 (:parent #41)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("webqtl" 0 6 (:parent #45))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("s" 0 1 (:parent #46))) #(", or\nchange the settings in etc/default" 0 39 (:parent #41)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("settings.py" 0 11 (:parent #48))) #("to match your path.\n" 0 20 (:parent #41)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #18]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #24)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #24))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #21] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #19))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #19]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #22]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #25))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #22] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #26))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #20))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #20]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #23]) #("See " 0 4 (:parent #26)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #26] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #26))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #21))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #21]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #27)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #27] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #27))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #22))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #25))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #25]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #28]) #("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 #31)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("PATH" 0 4 (:parent #35))) #("and R" 0 5 (:parent #31)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("LIBS" 0 4 (:parent #37))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #31] :use-brackets-p nil) #("SITE" 0 4 (:parent #38))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #31))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #28] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #28]) #("On one system:\n" 0 15 (:parent #33))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #28] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #28]) #("and perhaps a few more.\n" 0 24 (:parent #35))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #26)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("data" 0 4 (:parent #38))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #26)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("files" 0 5 (:parent #40))) #("/genotype'" 0 10 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #26]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #29]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #32)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("data" 0 4 (:parent #36))) #(". 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 #32)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("settings.py" 0 11 (:parent #38))) #("(see above in\nthis document).\n" 0 30 (:parent #32))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #29]) #("You can use the GENENETWORK" 0 27 (:parent #33)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #33] :use-brackets-p nil) #("FILES" 0 5 (:parent #37))) #("switch to set the datadir, for example\n" 0 39 (:parent #33))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #29] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #27))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #27]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #30]) #("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 #33))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #28))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #28]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #31]) #("This error\n" 0 11 (:parent #34))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #31] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("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 #36))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #31]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #37)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("LIBS" 0 4 (:parent #41))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #37] :use-brackets-p nil) #("SITE" 0 4 (:parent #42))) #(". 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 #37))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #22] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #29))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #29]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #32]) #("The following error\n" 0 20 (:parent #35))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #32] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("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 #37))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #39))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #32]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #41)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #41] :use-brackets-p nil) #("URI" 0 3 (:parent #45))) #("to something like\n" 0 18 (:parent #41))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #32] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #5] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #23))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #23] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #26))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 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 #9)) (link (:standard-properties [1672 nil 1734 1744 1746 0 nil nil nil nil nil nil nil nil # nil nil #9] :type "https" :type-explicit-p t :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) #("Guix-notes" 0 10 (:parent #15))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #9))) (paragraph (:standard-properties [1829 1829 1829 2178 2179 1 nil nil nil nil nil nil nil nil # nil nil #6]) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #12)) (subscript (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #12] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #18))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #12] :use-brackets-p nil) #("PATH" 0 4 (:parent #19))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #12))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #9] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #9]) #("It should upgrade (ignore the locales warnings). 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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 (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #24))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #20)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #20] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #20] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #20))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #9] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #7))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #7]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #10]) #("Check out the source with git:\n" 0 31 (:parent #13))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #10] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #15))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #10] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #18))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #10]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #20))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #10]) #("And browse on your local machine to " 0 36 (:parent #21)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #21))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #8))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #8]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #11]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. 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Note it may already be running on our servers!\n" 0 49 (:parent #14))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #9))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #9]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #12]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #15))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # 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nil nil #16] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #31))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("When you get errors like:\n" 0 26 (:parent #33))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #16]) #("you may need to set\n" 0 20 (:parent #35))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #16] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #10] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #14))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #14]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #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 (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("webqtl" 0 6 (:parent #24))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("s" 0 1 (:parent #25))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #20)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("webqtl" 0 6 (:parent #27))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #20] :use-brackets-p nil) #("plant" 0 5 (:parent #28))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #20))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Download one database from\n" 0 27 (:parent #21))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #17]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #22))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #23))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #17] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #25))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("and\n" 0 4 (:parent #28))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #30))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #17] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #17]) #("Note for the plant database you can rename it to db" 0 51 (:parent #34)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("webqtl" 0 6 (:parent #38))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("s" 0 1 (:parent #39))) #(", or\nchange the settings in etc/default" 0 39 (:parent #34)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #34] :use-brackets-p nil) #("settings.py" 0 11 (:parent #41))) #("to match your path.\n" 0 20 (:parent #34)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #11))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #11]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #14]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #17)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #17] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #17))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #14] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #12]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #15]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #18))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #15] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #19] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #19))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #13))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #13]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #16]) #("See " 0 4 (:parent #19)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #19] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #19))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #14]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #20)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #20] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #20))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #18))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #18]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #21]) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. 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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 (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #25] :use-brackets-p nil) #("settings.py" 0 11 (:parent #31))) #("(see above in\nthis document).\n" 0 30 (:parent #25))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #22]) #("You can use the GENENETWORK" 0 27 (:parent #26)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("FILES" 0 5 (:parent #30))) #("switch to set the datadir, for example\n" 0 39 (:parent #26))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #22] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #20))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #20]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #23]) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. 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Please check with the authors when a module\nis missing.\n" 0 211 (:parent #26))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #21]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("This error\n" 0 11 (:parent #27))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #30)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("LIBS" 0 4 (:parent #34))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #30] :use-brackets-p nil) #("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 (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #15] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #22))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #22]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #25]) #("The following error\n" 0 20 (:parent #28))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #25] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #25]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil #25] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil (org-data (:standard-properties [1 1 1 13242 13242 0 nil org-data nil nil nil 3 13242 nil # nil nil nil] :path nil :CATEGORY nil) . #0)] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #16] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #19))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # 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Debian-derived distros\nmay support\n" 0 117 (:parent #13))) (fixed-width (:standard-properties [2885 2885 nil nil 2909 2 nil nil nil nil nil nil nil nil # nil nil #10] :value "apt-get install guix")))) (headline (:standard-properties [2909 2909 2940 4939 4939 0 (:title) nil nil nil nil 2942 4937 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 29) t] :title (#("Creating a GNU Guix profile" 0 27 (:parent #8))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [2940 2940 2940 4939 4939 0 nil section nil nil nil 2940 4939 nil # nil nil #8]) (paragraph (:standard-properties [2940 2940 2940 3216 3217 1 nil planning nil nil nil nil nil nil # nil nil #11]) #("We run a GNU Guix channel with packages at " 0 43 (:parent #14)) (link (:standard-properties [2983 nil 3054 3073 3075 0 nil nil nil nil nil nil nil nil # nil nil #14] :type "https" :type-explicit-p t :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) #("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 (:standard-properties [3157 nil 3158 3165 3165 0 nil nil nil nil nil nil nil nil # nil nil #14] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #20))) (subscript (:standard-properties [3165 nil 3166 3170 3171 1 nil nil nil nil nil nil nil nil # nil nil #14] :use-brackets-p nil) #("PATH" 0 4 (:parent #21))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #14))) (fixed-width (:standard-properties [3217 3217 nil nil 3263 2 nil nil nil nil nil nil nil nil # nil nil #11] :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull")) (paragraph (:standard-properties [3263 3263 3263 3379 3380 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [3380 3380 nil nil 3429 2 nil nil nil nil nil nil nil nil # nil nil #11] :value "guix pull -p ~/opt/guix-pull --commit=f04883d")) (paragraph (:standard-properties [3429 3429 3429 3570 3571 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #11] :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")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #11]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #20))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #11] :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")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #26))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #22)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #22] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #22))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #11] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #9))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #9]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #12]) #("Check out the source with git:\n" 0 31 (:parent #15))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #12] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #17))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #12] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #20))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #12]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #22))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #12]) #("And browse on your local machine to " 0 36 (:parent #23)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #23))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #10))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #10]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #13]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #16)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #16] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #20))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #16))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #11))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #11]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #14]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #17))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #0] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #12))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #12] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #15))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #15]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #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 (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("As root configure the Guix profile\n" 0 35 (:parent #22))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #18] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("and run for example\n" 0 20 (:parent #24))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #18] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("If you want to run as root you may have to set\n" 0 47 (:parent #26))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("You also need to set\n" 0 21 (:parent #28))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #30))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #31))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #33))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("When you get errors like:\n" 0 26 (:parent #35))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #18]) #("you may need to set\n" 0 20 (:parent #37))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #18] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #12] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #16))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #16]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #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 (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("webqtl" 0 6 (:parent #26))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("s" 0 1 (:parent #27))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #22)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("webqtl" 0 6 (:parent #29))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #22] :use-brackets-p nil) #("plant" 0 5 (:parent #30))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #22))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("Download one database from\n" 0 27 (:parent #23))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #19]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #24))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #25))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #19] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #27))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #19] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #19] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("and\n" 0 4 (:parent #30))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #19] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #32))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #19] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #19]) #("Note for the plant database you can rename it to db" 0 51 (:parent #36)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("webqtl" 0 6 (:parent #40))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("s" 0 1 (:parent #41))) #(", or\nchange the settings in etc/default" 0 39 (:parent #36)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #36] :use-brackets-p nil) #("settings.py" 0 11 (:parent #43))) #("to match your path.\n" 0 20 (:parent #36)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #13))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #13]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #16]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #19)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #19] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #19))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #16] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #14))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #14]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #17]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #20))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #17] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #21))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #15))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #15]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #18]) #("See " 0 4 (:parent #21)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #21] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #21))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #16))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #16]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #19]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #22)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #22))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #17))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #20))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #20]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #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 (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("PATH" 0 4 (:parent #30))) #("and R" 0 5 (:parent #26)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("LIBS" 0 4 (:parent #32))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #26] :use-brackets-p nil) #("SITE" 0 4 (:parent #33))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #26))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #23] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #23]) #("On one system:\n" 0 15 (:parent #28))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #23] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #23]) #("and perhaps a few more.\n" 0 24 (:parent #30))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #21)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("data" 0 4 (:parent #33))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #21)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #21] :use-brackets-p nil) #("files" 0 5 (:parent #35))) #("/genotype'" 0 10 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #21]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #24]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #27)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("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 (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #27] :use-brackets-p nil) #("settings.py" 0 11 (:parent #33))) #("(see above in\nthis document).\n" 0 30 (:parent #27))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #24]) #("You can use the GENENETWORK" 0 27 (:parent #28)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #28] :use-brackets-p nil) #("FILES" 0 5 (:parent #32))) #("switch to set the datadir, for example\n" 0 39 (:parent #28))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #24] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #22))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #22]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #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 (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #23))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #23]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #26]) #("This error\n" 0 11 (:parent #29))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #26] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #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 (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #26]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #32)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("LIBS" 0 4 (:parent #36))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #32] :use-brackets-p nil) #("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 (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #17] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #24))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #24]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #27]) #("The following error\n" 0 20 (:parent #30))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #27] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #27]) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. 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nil nil nil nil nil nil nil nil # nil nil #27] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #0] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #18))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #18] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #21))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred 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Author: %a (%e)

\n

Date: %d

\n

%c

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%v

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Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #362))) (fixed-width (:standard-properties [3571 3571 nil nil 3843 2 nil nil nil nil nil nil nil nil # nil nil #355] :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=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [3843 3843 3843 3919 3920 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #364))) (fixed-width (:standard-properties [3920 3920 nil nil 4154 2 nil nil nil nil nil nil nil nil # nil nil #355] :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2")) (paragraph (:standard-properties [4154 4154 4154 4554 4555 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #366)) (link (:standard-properties [4331 nil 4412 4423 4425 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :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) #("substitutes" 0 11 (:parent #370))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #366)) (link (:standard-properties [4463 nil nil nil 4491 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "http" :type-explicit-p t :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil)) (link (:standard-properties [4491 nil nil nil 4515 1 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil)) (link (:standard-properties [4515 nil nil nil 4543 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "https" :type-explicit-p t :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil)) #("\"` switch.\n" 0 11 (:parent #366))) (paragraph (:standard-properties [4555 4555 4555 4667 4668 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #367))) (src-block (:standard-properties [4668 4668 nil nil 4809 1 nil nil nil nil nil nil nil nil # nil nil #355] :language "scheme" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (19 130) t])) (paragraph (:standard-properties [4809 4809 4809 4938 4939 1 nil nil nil nil nil nil nil nil # nil nil #355]) #("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 #369))))) (headline (:standard-properties [4939 4939 4954 5820 5820 0 (:title) nil nil nil nil 4956 5818 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 13) t] :title (#("Running GN2" 0 11 (:parent #353))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [4954 4954 4954 5820 5820 0 nil section nil nil nil 4954 5820 nil # nil nil #353]) (paragraph (:standard-properties [4954 4954 4954 4985 4986 1 nil planning nil nil nil nil nil nil # nil nil #356]) #("Check out the source with git:\n" 0 31 (:parent #359))) (fixed-width (:standard-properties [4986 4986 nil nil 5061 2 nil nil nil nil nil nil nil nil # nil nil #356] :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2")) (paragraph (:standard-properties [5061 5061 5061 5093 5094 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("Run GN2 with above Guix profile\n" 0 32 (:parent #361))) (fixed-width (:standard-properties [5094 5094 nil nil 5387 2 nil nil nil nil nil nil nil nil # nil nil #356] :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")) (paragraph (:standard-properties [5387 5387 5387 5520 5521 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("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 #363))) (paragraph (:standard-properties [5521 5521 5521 5605 5606 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #364))) (paragraph (:standard-properties [5606 5606 5606 5691 5692 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #365))) (paragraph (:standard-properties [5692 5692 5692 5759 5760 1 nil nil nil nil nil nil nil nil # nil nil #356]) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #366))) (paragraph (:standard-properties [5760 5760 5760 5819 5820 1 nil nil nil nil nil nil nil nil # nil nil #356]) #("And browse on your local machine to " 0 36 (:parent #367)) (link (:standard-properties [5796 nil nil nil 5818 0 nil nil nil nil nil nil nil nil # nil nil #367] :type "http" :type-explicit-p t :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil)) #("\n" 0 1 (:parent #367))))) (headline (:standard-properties [5820 5820 5836 6058 6058 0 (:title) nil nil nil nil 5838 6056 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Run gn-proxy" 0 12 (:parent #354))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [5836 5836 5836 6058 6058 0 nil section nil nil nil 5836 6058 nil # nil nil #354]) (paragraph (:standard-properties [5836 5836 5836 6057 6058 1 nil planning nil nil nil nil nil nil # nil nil #357]) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #360)) (link (:standard-properties [5957 nil 6000 6006 6008 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "https" :type-explicit-p t :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil) #("README" 0 6 (:parent #364))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #360))))) (headline (:standard-properties [6058 6058 6071 6163 6163 0 (:title) nil nil nil nil 6073 6161 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Run Redis" 0 9 (:parent #355))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6071 6071 6071 6163 6163 0 nil section nil nil nil 6071 6163 nil # nil nil #355]) (paragraph (:standard-properties [6071 6071 6071 6162 6163 1 nil planning nil nil nil nil nil nil # nil nil #358]) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #361))))) (headline (:standard-properties [6163 6163 6184 9262 9262 0 (:title) nil nil nil nil 6186 9260 1 # nil nil #344] :pre-blank 0 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Run MariaDB server" 0 18 (:parent #356))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [6184 6184 6218 7711 7711 0 (:title) section nil nil nil 6220 7709 2 # nil nil #356] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 32) t] :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #359))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [6218 6218 6218 7711 7711 0 nil section nil nil nil 6218 7711 nil # nil nil #359]) (paragraph (:standard-properties [6218 6218 6218 6354 6355 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("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 #365))) (paragraph (:standard-properties [6355 6355 6355 6390 6391 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("As root configure the Guix profile\n" 0 35 (:parent #366))) (fixed-width (:standard-properties [6391 6391 nil nil 6427 2 nil nil nil nil nil nil nil nil # nil nil #362] :value ". ~/opt/genenetwork2/etc/profile")) (paragraph (:standard-properties [6427 6427 6427 6447 6448 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("and run for example\n" 0 20 (:parent #368))) (src-block (:standard-properties [6448 6448 nil nil 6936 1 nil nil nil nil nil nil nil nil # nil nil #362] :language "bash" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (17 477) t])) (paragraph (:standard-properties [6936 6936 6936 6983 6984 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("If you want to run as root you may have to set\n" 0 47 (:parent #370))) (fixed-width (:standard-properties [6984 6984 nil nil 7024 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/etc/my.cnf\n[mariadbd]\nuser=root")) (paragraph (:standard-properties [7024 7024 7024 7045 7046 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("You also need to set\n" 0 21 (:parent #372))) (fixed-width (:standard-properties [7046 7046 nil nil 7069 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "ft_min_word_len = 3")) (paragraph (:standard-properties [7069 7069 7069 7148 7149 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #374))) (paragraph (:standard-properties [7149 7149 7149 7217 7218 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #375))) (fixed-width (:standard-properties [7218 7218 nil nil 7333 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log")) (paragraph (:standard-properties [7333 7333 7333 7410 7411 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #377))) (fixed-width (:standard-properties [7411 7411 nil nil 7521 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb")) (paragraph (:standard-properties [7521 7521 7521 7547 7548 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("When you get errors like:\n" 0 26 (:parent #379))) (fixed-width (:standard-properties [7548 7548 nil nil 7662 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')")) (paragraph (:standard-properties [7662 7662 7662 7682 7683 1 nil nil nil nil nil nil nil nil # nil nil #362]) #("you may need to set\n" 0 20 (:parent #381))) (fixed-width (:standard-properties [7683 7683 nil nil 7711 2 nil nil nil nil nil nil nil nil # nil nil #362] :value "set foreign_key_checks=0")))) (headline (:standard-properties [7711 7711 7748 9262 9262 0 (:title) nil nil nil nil 7750 9260 2 # nil nil #356] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 35) t] :title (#("Load the small database in MySQL" 0 32 (:parent #360))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [7748 7748 7748 9262 9262 0 nil section nil nil nil 7748 9262 nil # nil nil #360]) (paragraph (:standard-properties [7748 7748 7748 8054 8055 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("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 #366)) (subscript (:standard-properties [7911 nil 7912 7918 7918 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("webqtl" 0 6 (:parent #370))) (subscript (:standard-properties [7918 nil 7919 7920 7920 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("s" 0 1 (:parent #371))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #366)) (subscript (:standard-properties [7996 nil 7997 8003 8003 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("webqtl" 0 6 (:parent #373))) (subscript (:standard-properties [8003 nil 8004 8009 8009 0 nil nil nil nil nil nil nil nil # nil nil #366] :use-brackets-p nil) #("plant" 0 5 (:parent #374))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #366))) (paragraph (:standard-properties [8055 8055 8055 8082 8083 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("Download one database from\n" 0 27 (:parent #367))) (paragraph (:standard-properties [8083 8083 8083 8163 8164 1 nil nil nil nil nil nil nil nil # nil nil #363]) (link (:standard-properties [8083 nil nil nil 8162 0 nil nil nil nil nil nil nil nil # nil nil #368] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil)) #("\n" 0 1 (:parent #368))) (paragraph (:standard-properties [8164 8164 8164 8232 8233 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #369))) (src-block (:standard-properties [8233 8233 nil nil 8375 1 nil nil nil nil nil nil nil nil # nil nil #363] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 131) t])) (paragraph (:standard-properties [8375 8375 8375 8421 8422 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #371))) (fixed-width (:standard-properties [8422 8422 nil nil 8455 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "mysql_upgrade -u root --force")) (fixed-width (:standard-properties [8455 8455 nil nil 8472 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "myslq -u root")) (paragraph (:standard-properties [8472 8472 8472 8476 8477 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("and\n" 0 4 (:parent #374))) (fixed-width (:standard-properties [8477 8477 nil nil 8703 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+")) (paragraph (:standard-properties [8703 8703 8703 8767 8768 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #376))) (fixed-width (:standard-properties [8768 8768 nil nil 8859 2 nil nil nil nil nil nil nil nil # nil nil #363] :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';")) (paragraph (:standard-properties [8859 8859 8859 8965 8966 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #378))) (paragraph (:standard-properties [8966 8966 8966 9128 9129 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("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 #379))) (paragraph (:standard-properties [9129 9129 9129 9261 9262 1 nil nil nil nil nil nil nil nil # nil nil #363]) #("Note for the plant database you can rename it to db" 0 51 (:parent #380)) (subscript (:standard-properties [9180 nil 9181 9187 9187 0 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("webqtl" 0 6 (:parent #384))) (subscript (:standard-properties [9187 nil 9188 9189 9189 0 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("s" 0 1 (:parent #385))) #(", or\nchange the settings in etc/default" 0 39 (:parent #380)) (subscript (:standard-properties [9228 nil 9229 9240 9241 1 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("settings.py" 0 11 (:parent #387))) #("to match your path.\n" 0 20 (:parent #380)))))) (headline (:standard-properties [9262 9262 9284 9504 9504 0 (:title) nil nil nil nil 9286 9502 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 20) t] :title (#("Get genotype files" 0 18 (:parent #357))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9284 9284 9284 9504 9504 0 nil section nil nil nil 9284 9504 nil # nil nil #357]) (paragraph (:standard-properties [9284 9284 9284 9422 9423 1 nil planning nil nil nil nil nil nil # nil nil #360]) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #363)) (link (:standard-properties [9342 nil nil nil 9421 0 nil nil nil nil nil nil nil nil # nil nil #363] :type "http" :type-explicit-p t :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil)) #("\n" 0 1 (:parent #363))) (src-block (:standard-properties [9423 9423 nil nil 9504 1 nil nil nil nil nil nil nil nil # nil nil #360] :language "sh" :switches nil :parameters nil :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (15 70) t])))) (headline (:standard-properties [9504 9504 9528 9668 9668 0 (:title) nil nil nil nil 9530 9666 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 22) t] :title (#("GN2 Dependency Graph" 0 20 (:parent #358))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9528 9528 9528 9668 9668 0 nil section nil nil nil 9528 9668 nil # nil nil #358]) (paragraph (:standard-properties [9528 9528 9528 9588 9589 1 nil planning nil nil nil nil nil nil # nil nil #361]) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #364))) (paragraph (:standard-properties [9589 9619 9619 9667 9668 1 nil nil nil nil nil nil nil nil # nil nil #361] :attr_html (":title GN2_graph")) (link (:standard-properties [9619 nil nil nil 9666 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "http" :type-explicit-p t :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil)) #("\n" 0 1 (:parent #365))))) (headline (:standard-properties [9668 9668 9704 9730 9730 0 (:title) nil nil nil nil 9706 9728 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 34) t] :title (#("Working with the GN2 source code" 0 32 (:parent #359))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9704 9704 9704 9730 9730 0 nil section nil nil nil 9704 9730 nil # nil nil #359]) (paragraph (:standard-properties [9704 9704 9704 9729 9730 1 nil planning nil nil nil nil nil nil # nil nil #362]) #("See " 0 4 (:parent #365)) (link (:standard-properties [9708 nil nil nil 9727 0 nil nil nil nil nil nil nil nil # nil nil #365] :type "fuzzy" :type-explicit-p nil :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil)) #(".\n" 0 2 (:parent #365))))) (headline (:standard-properties [9730 9730 9743 9880 9880 0 (:title) nil nil nil nil 9745 9878 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 11) t] :title (#("Read more" 0 9 (:parent #360))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9743 9743 9743 9880 9880 0 nil section nil nil nil 9743 9880 nil # nil nil #360]) (paragraph (:standard-properties [9743 9743 9743 9879 9880 1 nil planning nil nil nil nil nil nil # nil nil #363]) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #366)) (link (:standard-properties [9798 nil nil nil 9818 0 nil nil nil nil nil nil nil nil # nil nil #366] :type "fuzzy" :type-explicit-p nil :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #366))))) (headline (:standard-properties [9880 9880 9900 12330 12330 0 (:title) nil nil nil nil 9902 12328 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 18) t] :title (#("Trouble shooting" 0 16 (:parent #361))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [9900 9900 9940 10434 10434 0 (:title) section nil nil nil 9942 10432 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 38) t] :title (#("ImportError: No module named jinja2" 0 35 (:parent #364))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [9940 9940 9940 10434 10434 0 nil section nil nil nil 9940 10434 nil # nil nil #364]) (paragraph (:standard-properties [9940 9940 9940 10174 10175 1 nil planning nil nil nil nil nil nil # nil nil #367]) #("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 #370)) (subscript (:standard-properties [10107 nil 10108 10112 10113 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("PATH" 0 4 (:parent #374))) #("and R" 0 5 (:parent #370)) (subscript (:standard-properties [10118 nil 10119 10123 10123 0 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("LIBS" 0 4 (:parent #376))) (subscript (:standard-properties [10123 nil 10124 10128 10129 1 nil nil nil nil nil nil nil nil # nil nil #370] :use-brackets-p nil) #("SITE" 0 4 (:parent #377))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #370))) (fixed-width (:standard-properties [10175 10175 nil nil 10206 2 nil nil nil nil nil nil nil nil # nil nil #367] :value "guix package --search-paths")) (paragraph (:standard-properties [10206 10206 10206 10221 10222 1 nil nil nil nil nil nil nil nil # nil nil #367]) #("On one system:\n" 0 15 (:parent #372))) (fixed-width (:standard-properties [10222 10222 nil nil 10410 2 nil nil nil nil nil nil nil nil # nil nil #367] :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\"")) (paragraph (:standard-properties [10410 10410 10410 10434 10434 0 nil nil nil nil nil nil nil nil # nil nil #367]) #("and perhaps a few more.\n" 0 24 (:parent #374))))) (headline (:standard-properties [10434 10434 10543 10930 10930 0 (:title) nil nil nil nil 10545 10928 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 107) t] :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #365)) (subscript (:standard-properties [10477 nil 10478 10482 10482 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("data" 0 4 (:parent #377))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #365)) (subscript (:standard-properties [10525 nil 10526 10531 10531 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("files" 0 5 (:parent #379))) #("/genotype'" 0 10 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10543 10543 10543 10930 10930 0 nil section nil nil nil 10543 10930 nil # nil nil #365]) (paragraph (:standard-properties [10543 10543 10543 10764 10765 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #371)) (subscript (:standard-properties [10592 nil 10593 10597 10597 0 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("data" 0 4 (:parent #375))) #(". 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 #371)) (subscript (:standard-properties [10721 nil 10722 10733 10734 1 nil nil nil nil nil nil nil nil # nil nil #371] :use-brackets-p nil) #("settings.py" 0 11 (:parent #377))) #("(see above in\nthis document).\n" 0 30 (:parent #371))) (paragraph (:standard-properties [10765 10765 10765 10838 10839 1 nil nil nil nil nil nil nil nil # nil nil #368]) #("You can use the GENENETWORK" 0 27 (:parent #372)) (subscript (:standard-properties [10792 nil 10793 10798 10799 1 nil nil nil nil nil nil nil nil # nil nil #372] :use-brackets-p nil) #("FILES" 0 5 (:parent #376))) #("switch to set the datadir, for example\n" 0 39 (:parent #372))) (fixed-width (:standard-properties [10839 10839 nil nil 10930 2 nil nil nil nil nil nil nil nil # nil nil #368] :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2")))) (headline (:standard-properties [10930 10930 10953 11164 11164 0 (:title) nil nil nil nil 10955 11162 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 21) t] :title (#("Can't run a module" 0 18 (:parent #366))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [10953 10953 10953 11164 11164 0 nil section nil nil nil 10953 11164 nil # nil nil #366]) (paragraph (:standard-properties [10953 10953 10953 11164 11164 0 nil planning nil nil nil nil nil nil # nil nil #369]) #("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 #372))))) (headline (:standard-properties [11164 11164 11196 11665 11665 0 (:title) nil nil nil nil 11198 11663 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 30) t] :title (#("Rpy2 error 'show' now found" 0 27 (:parent #367))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11196 11196 11196 11665 11665 0 nil section nil nil nil 11196 11665 nil # nil nil #367]) (paragraph (:standard-properties [11196 11196 11196 11207 11208 1 nil planning nil nil nil nil nil nil # nil nil #370]) #("This error\n" 0 11 (:parent #373))) (fixed-width (:standard-properties [11208 11208 nil nil 11288 2 nil nil nil nil nil nil nil nil # nil nil #370] :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found")) (paragraph (:standard-properties [11288 11288 11288 11418 11419 1 nil nil nil nil nil nil nil nil # nil nil #370]) #("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 #375))) (paragraph (:standard-properties [11419 11419 11419 11664 11665 1 nil nil nil nil nil nil nil nil # nil nil #370]) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #376)) (subscript (:standard-properties [11482 nil 11483 11487 11487 0 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("LIBS" 0 4 (:parent #380))) (subscript (:standard-properties [11487 nil 11488 11492 11492 0 nil nil nil nil nil nil nil nil # nil nil #376] :use-brackets-p nil) #("SITE" 0 4 (:parent #381))) #(". 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 #376))))) (headline (:standard-properties [11665 11665 11717 12330 12330 0 (:title) nil nil nil nil 11719 12328 2 # nil nil #361] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 50) t] :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #368))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [11717 11717 11717 12330 12330 0 nil section nil nil nil 11717 12330 nil # nil nil #368]) (paragraph (:standard-properties [11717 11717 11717 11737 11738 1 nil planning nil nil nil nil nil nil # nil nil #371]) #("The following error\n" 0 20 (:parent #374))) (fixed-width (:standard-properties [11738 11738 nil nil 11933 2 nil nil nil nil nil nil nil nil # nil nil #371] :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\")')")) (paragraph (:standard-properties [11933 11933 11933 12090 12091 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("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 #376))) (fixed-width (:standard-properties [12091 12091 nil nil 12113 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h localhost")) (paragraph (:standard-properties [12113 12113 12113 12169 12170 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #378))) (fixed-width (:standard-properties [12170 12170 nil nil 12192 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "mysql -h 127.0.0.1")) (paragraph (:standard-properties [12192 12192 12192 12262 12263 1 nil nil nil nil nil nil nil nil # nil nil #371]) #("if that works run genenetwork after setting SQL" 0 47 (:parent #380)) (subscript (:standard-properties [12239 nil 12240 12243 12244 1 nil nil nil nil nil nil nil nil # nil nil #380] :use-brackets-p nil) #("URI" 0 3 (:parent #384))) #("to something like\n" 0 18 (:parent #380))) (fixed-width (:standard-properties [12263 12263 nil nil 12330 2 nil nil nil nil nil nil nil nil # nil nil #371] :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s"))))) (headline (:standard-properties [12330 12330 12339 13242 13242 0 (:title) nil nil nil nil 12341 13240 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 7) t] :title (#("NOTES" 0 5 (:parent #362))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (headline (:standard-properties [12339 12339 12366 13242 13242 0 (:title) section nil nil nil 12368 13240 2 # nil nil #362] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (3 25) t] :title (#("Deploying GN2 official" 0 22 (:parent #365))) :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [12366 12366 12366 13242 13242 0 nil section nil nil nil 12366 13242 nil # nil nil #365]) (paragraph (:standard-properties [12366 12366 12366 12421 12422 1 nil planning nil nil nil nil nil nil # nil nil #368]) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #371))) (plain-list (:standard-properties [12422 12422 12422 13242 13242 0 nil nil nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #368] :type unordered) (item (:standard-properties [12422 12422 12428 13242 13242 0 (:tag) item nil nil nil nil nil nil # 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nil nil #394] :type "http" :type-explicit-p t :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil)) #("\n" 0 1 (:parent #394)))) (item (:standard-properties [12702 12702 12712 12780 12780 0 (:tag) item nil nil nil nil nil nil # nil ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 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)) #387] :bullet "- " :checkbox off :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [12712 12712 12712 12780 12780 0 nil nil nil nil nil nil nil nil # 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generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-02-07 14:55:29 +0000