Error: user-error ("Unable to resolve link: \"introduction\"")
mapbacktrace(#f(compiled-function (evald func args flags) #))
debug-early-backtrace()
debug-early(error (user-error "Unable to resolve link: \"introduction\""))
signal(user-error ("Unable to resolve link: \"introduction\""))
user-error("Unable to resolve link: %S" "introduction")
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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1672 :end 1746 :contents-begin 1734 :contents-end 1744 :post-blank 0 :parent #183) #("Guix-notes" 0 10 (:parent #189))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #183))) (paragraph (:begin 1829 :end 2179 :contents-begin 1829 :contents-end 2178 :post-blank 1 :post-affiliated 1829 :mode nil :granularity nil :parent #180) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 2047 :end 2123 :contents-begin 2101 :contents-end 2120 :post-blank 1 :parent #184) #("Guix bioinformatics" 0 19 (:parent #188))) #("and " 0 4 (:parent #184)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2127 :end 2176 :contents-begin 2166 :contents-end 2174 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2179 :end 2314 :contents-begin 2179 :contents-end 2314 :post-blank 0 :post-affiliated 2179 :mode nil :granularity nil :parent #180) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #185)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2265 :end 2312 :contents-begin 2290 :contents-end 2310 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Check list" :begin 2315 :end 2584 :pre-blank 1 :contents-begin 2329 :contents-end 2583 :robust-begin 2331 :robust-end 2581 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2315 :title (#("Check list" 0 10 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2329 :end 2584 :contents-begin 2329 :contents-end 2583 :robust-begin 2329 :robust-end 2581 :post-blank 1 :post-affiliated 2329 :mode section :granularity nil :parent #178) (paragraph (:begin 2329 :end 2390 :contents-begin 2329 :contents-end 2389 :post-blank 1 :post-affiliated 2329 :mode planning :granularity nil :parent #181) #("To run GeneNetwork the following services need to function:\n" 0 60 (:parent #184))) (plain-list (:type ordered :begin 2390 :end 2583 :contents-begin 2390 :contents-end 2583 :structure ((2390 0 "1. 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" :begin 2443 :end 2488 :contents-begin 2450 :contents-end 2488 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2443 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2450 :end 2488 :contents-begin 2450 :contents-end 2488 :post-blank 0 :post-affiliated 2450 :mode nil :granularity nil :parent #189) #("A path to the (static) genotype files\n" 0 38 (:parent #192)))) (item (:bullet "1. " :begin 2488 :end 2523 :contents-begin 2495 :contents-end 2523 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2488 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2495 :end 2523 :contents-begin 2495 :contents-end 2523 :post-blank 0 :post-affiliated 2495 :mode nil :granularity nil :parent #190) #("Gn-proxy for authentication\n" 0 28 (:parent #193)))) (item (:bullet "1. " :begin 2523 :end 2555 :contents-begin 2530 :contents-end 2555 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2523 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2530 :end 2555 :contents-begin 2530 :contents-end 2555 :post-blank 0 :post-affiliated 2530 :mode nil :granularity nil :parent #191) #("The genenetwork3 service\n" 0 25 (:parent #194)))) (item (:bullet "1. " :begin 2555 :end 2568 :contents-begin 2562 :contents-end 2568 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2555 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2562 :end 2568 :contents-begin 2562 :contents-end 2568 :post-blank 0 :post-affiliated 2562 :mode nil :granularity nil :parent #192) #("Redis\n" 0 6 (:parent #195)))) (item (:bullet "1. " :begin 2568 :end 2583 :contents-begin 2575 :contents-end 2583 :checkbox off :counter nil :structure ((2390 0 "1. " nil "[ ]" nil 2443) (2443 0 "1. " nil "[ ]" nil 2488) (2488 0 "1. " nil "[ ]" nil 2523) (2523 0 "1. " nil "[ ]" nil 2555) (2555 0 "1. " nil "[ ]" nil 2568) (2568 0 "1. " nil "[ ]" nil 2583)) :pre-blank 0 :post-blank 0 :post-affiliated 2568 :tag nil :mode item :granularity nil :parent #185) (paragraph (:begin 2575 :end 2583 :contents-begin 2575 :contents-end 2583 :post-blank 0 :post-affiliated 2575 :mode nil :granularity nil :parent #193) #("Mariadb\n" 0 8 (:parent #196))))))) (headline (:raw-value "Installing Guix packages" :begin 2584 :end 2909 :pre-blank 1 :contents-begin 2612 :contents-end 2908 :robust-begin 2614 :robust-end 2906 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2584 :title (#("Installing Guix packages" 0 24 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2612 :end 2909 :contents-begin 2612 :contents-end 2908 :robust-begin 2612 :robust-end 2906 :post-blank 1 :post-affiliated 2612 :mode section :granularity nil :parent #179) (paragraph (:begin 2612 :end 2885 :contents-begin 2612 :contents-end 2884 :post-blank 1 :post-affiliated 2612 :mode planning :granularity nil :parent #182) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #185)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2729 :end 2767 :contents-begin nil :contents-end nil :post-blank 1 :parent #185)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data. Debian-derived distros\nmay support\n" 0 117 (:parent #185))) (fixed-width (:begin 2885 :end 2908 :value "apt-get install guix" :post-blank 1 :post-affiliated 2885 :mode nil :granularity nil :parent #182)))) (headline (:raw-value "Creating a GNU Guix profile" :begin 2909 :end 4939 :pre-blank 1 :contents-begin 2940 :contents-end 4938 :robust-begin 2942 :robust-end 4936 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2909 :title (#("Creating a GNU Guix profile" 0 27 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2940 :end 4939 :contents-begin 2940 :contents-end 4938 :robust-begin 2940 :robust-end 4936 :post-blank 1 :post-affiliated 2940 :mode section :granularity nil :parent #180) (paragraph (:begin 2940 :end 3217 :contents-begin 2940 :contents-end 3216 :post-blank 1 :post-affiliated 2940 :mode planning :granularity nil :parent #183) #("We run a GNU Guix channel with packages at " 0 43 (:parent #186)) (link (:type "https" :path "//git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :format bracket :raw-link "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics" :application nil :search-option nil :begin 2983 :end 3075 :contents-begin 3054 :contents-end 3073 :post-blank 0 :parent #186) #("guix-bioinformatics" 0 19 (:parent #190))) #(". The\nREADME has instructions for hosting a channel, but typically we use\nthe GUIX" 0 82 (:parent #186)) (subscript (:begin 3157 :end 3165 :use-brackets-p nil :contents-begin 3158 :contents-end 3165 :post-blank 0 :parent #186) #("PACKAGE" 0 7 (:parent #192))) (subscript (:begin 3165 :end 3171 :use-brackets-p nil :contents-begin 3166 :contents-end 3170 :post-blank 1 :parent #186) #("PATH" 0 4 (:parent #193))) #("instead. First upgrade to a recent guix with\n" 0 45 (:parent #186))) (fixed-width (:begin 3217 :end 3263 :value "mkdir ~/opt\nguix pull -p ~/opt/guix-pull" :post-blank 2 :post-affiliated 3217 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3263 :end 3380 :contents-begin 3263 :contents-end 3379 :post-blank 1 :post-affiliated 3263 :mode nil :granularity nil :parent #183) #("It should upgrade (ignore the locales warnings). You can optionally\nspecify the specific git checkout of guix with\n" 0 116 (:parent #188))) (fixed-width (:begin 3380 :end 3429 :value "guix pull -p ~/opt/guix-pull --commit=f04883d" :post-blank 2 :post-affiliated 3380 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3429 :end 3571 :contents-begin 3429 :contents-end 3570 :post-blank 1 :post-affiliated 3429 :mode nil :granularity nil :parent #183) #("which is useful when you ned to roll back to an earlier version\n(sometimes our channel goes out of sync). Next, we install\nGeneNetwork2 with\n" 0 141 (:parent #190))) (fixed-width (:begin 3571 :end 3843 :value "source ~/opt/guix-pull/etc/profile\ngit clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics\ncd ~/guix-bioinformatics\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3571 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3843 :end 3920 :contents-begin 3843 :contents-end 3919 :post-blank 1 :post-affiliated 3843 :mode nil :granularity nil :parent #183) #("you probably also need guix-past (the upstream channel for older packages):\n" 0 76 (:parent #192))) (fixed-width (:begin 3920 :end 4154 :value "git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past\ncd ~/guix-past\nenv GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2" :post-blank 2 :post-affiliated 3920 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4154 :end 4555 :contents-begin 4154 :contents-end 4554 :post-blank 1 :post-affiliated 4154 :mode nil :granularity nil :parent #183) #("ignore the warnings. Guix should install the software without trying\nto build everything. If you system insists on building all packages,\ntry the `--dry-run` switch and fix the " 0 177 (:parent #194)) (link (:type "https" :path "//guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :format bracket :raw-link "https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html" :application nil :search-option nil :begin 4331 :end 4425 :contents-begin 4412 :contents-end 4423 :post-blank 0 :parent #194) #("substitutes" 0 11 (:parent #198))) #(". You may add the\n`--substitute-urls=\"" 0 38 (:parent #194)) (link (:type "http" :path "//guix.genenetwork.org" :format plain :raw-link "http://guix.genenetwork.org" :application nil :search-option nil :begin 4463 :end 4491 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//ci.guix.gnu.org" :format plain :raw-link "https://ci.guix.gnu.org" :application nil :search-option nil :begin 4491 :end 4515 :contents-begin nil :contents-end nil :post-blank 1 :parent #194)) (link (:type "https" :path "//mirror.hydra.gnu.org" :format plain :raw-link "https://mirror.hydra.gnu.org" :application nil :search-option nil :begin 4515 :end 4543 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\"` switch.\n" 0 11 (:parent #194))) (paragraph (:begin 4555 :end 4668 :contents-begin 4555 :contents-end 4667 :post-blank 1 :post-affiliated 4555 :mode nil :granularity nil :parent #183) #("The guix.genenetwork.org has most of our packages pre-built(!). To use\nit on your own machine the public key is\n" 0 112 (:parent #195))) (src-block (:language "scheme" :switches nil :parameters nil :begin 4668 :end 4809 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(public-key\n (ecc\n (curve Ed25519)\n (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))\n" :post-blank 1 :post-affiliated 4668 :mode nil :granularity nil :parent #183)) (paragraph (:begin 4809 :end 4938 :contents-begin 4809 :contents-end 4938 :post-blank 0 :post-affiliated 4809 :mode nil :granularity nil :parent #183) #("Once we have a GNU Guix profile, a running database (see below) and the file storage,\nwe should be ready to fire up GeneNetwork:\n" 0 129 (:parent #197))))) (headline (:raw-value "Running GN2" :begin 4939 :end 5820 :pre-blank 1 :contents-begin 4954 :contents-end 5819 :robust-begin 4956 :robust-end 5817 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4939 :title (#("Running GN2" 0 11 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 4954 :end 5820 :contents-begin 4954 :contents-end 5819 :robust-begin 4954 :robust-end 5817 :post-blank 1 :post-affiliated 4954 :mode section :granularity nil :parent #181) (paragraph (:begin 4954 :end 4986 :contents-begin 4954 :contents-end 4985 :post-blank 1 :post-affiliated 4954 :mode planning :granularity nil :parent #184) #("Check out the source with git:\n" 0 31 (:parent #187))) (fixed-width (:begin 4986 :end 5061 :value "git clone git@github.com:genenetwork/genenetwork2.git\ncd genenetwork2" :post-blank 2 :post-affiliated 4986 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5061 :end 5094 :contents-begin 5061 :contents-end 5093 :post-blank 1 :post-affiliated 5061 :mode nil :granularity nil :parent #184) #("Run GN2 with above Guix profile\n" 0 32 (:parent #189))) (fixed-width (:begin 5094 :end 5387 :value "export GN2_PROFILE=$HOME/opt/genenetwork2\nenv TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev" :post-blank 2 :post-affiliated 5094 :mode nil :granularity nil :parent #184)) (paragraph (:begin 5387 :end 5521 :contents-begin 5387 :contents-end 5520 :post-blank 1 :post-affiliated 5387 :mode nil :granularity nil :parent #184) #("the debug and logging switches can be particularly useful when\ndeveloping GN2. Location and files are the current ones for Penguin2.\n" 0 133 (:parent #191))) (paragraph (:begin 5521 :end 5606 :contents-begin 5521 :contents-end 5605 :post-blank 1 :post-affiliated 5521 :mode nil :granularity nil :parent #184) #("It may be useful to tunnel the web server to your local browser with\nan ssh tunnel:\n" 0 84 (:parent #192))) (paragraph (:begin 5606 :end 5692 :contents-begin 5606 :contents-end 5691 :post-blank 1 :post-affiliated 5606 :mode nil :granularity nil :parent #184) #("If you want to test a service running on the server on a certain\nport (say 8202) use\n" 0 85 (:parent #193))) (paragraph (:begin 5692 :end 5760 :contents-begin 5692 :contents-end 5759 :post-blank 1 :post-affiliated 5692 :mode nil :granularity nil :parent #184) #(" ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org\n" 0 67 (:parent #194))) (paragraph (:begin 5760 :end 5819 :contents-begin 5760 :contents-end 5819 :post-blank 0 :post-affiliated 5760 :mode nil :granularity nil :parent #184) #("And browse on your local machine to " 0 36 (:parent #195)) (link (:type "http" :path "//localhost:8202/" :format plain :raw-link "http://localhost:8202/" :application nil :search-option nil :begin 5796 :end 5818 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #("\n" 0 1 (:parent #195))))) (headline (:raw-value "Run gn-proxy" :begin 5820 :end 6058 :pre-blank 1 :contents-begin 5836 :contents-end 6057 :robust-begin 5838 :robust-end 6055 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5820 :title (#("Run gn-proxy" 0 12 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 5836 :end 6058 :contents-begin 5836 :contents-end 6057 :robust-begin 5836 :robust-end 6055 :post-blank 1 :post-affiliated 5836 :mode section :granularity nil :parent #182) (paragraph (:begin 5836 :end 6057 :contents-begin 5836 :contents-end 6057 :post-blank 0 :post-affiliated 5836 :mode planning :granularity nil :parent #185) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the\n" 0 121 (:parent #188)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 5957 :end 6008 :contents-begin 6000 :contents-end 6006 :post-blank 0 :parent #188) #("README" 0 6 (:parent #192))) #(". Note it may already be running on our servers!\n" 0 49 (:parent #188))))) (headline (:raw-value "Run Redis" :begin 6058 :end 6163 :pre-blank 1 :contents-begin 6071 :contents-end 6162 :robust-begin 6073 :robust-end 6160 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6058 :title (#("Run Redis" 0 9 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 6071 :end 6163 :contents-begin 6071 :contents-end 6162 :robust-begin 6071 :robust-end 6160 :post-blank 1 :post-affiliated 6071 :mode section :granularity nil :parent #183) (paragraph (:begin 6071 :end 6162 :contents-begin 6071 :contents-end 6162 :post-blank 0 :post-affiliated 6071 :mode planning :granularity nil :parent #186) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #189))))) (headline (:raw-value "Run MariaDB server" :begin 6163 :end 9262 :pre-blank 0 :contents-begin 6184 :contents-end 9261 :robust-begin 6186 :robust-end 9259 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6163 :title (#("Run MariaDB server" 0 18 (:parent #184))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 6184 :end 7711 :pre-blank 1 :contents-begin 6218 :contents-end 7710 :robust-begin 6220 :robust-end 7708 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6184 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #187))) :mode section :granularity nil :parent #184) (section (:begin 6218 :end 7711 :contents-begin 6218 :contents-end 7710 :robust-begin 6218 :robust-end 7708 :post-blank 1 :post-affiliated 6218 :mode section :granularity nil :parent #187) (paragraph (:begin 6218 :end 6355 :contents-begin 6218 :contents-end 6354 :post-blank 1 :post-affiliated 6218 :mode planning :granularity nil :parent #190) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #193))) (paragraph (:begin 6355 :end 6391 :contents-begin 6355 :contents-end 6390 :post-blank 1 :post-affiliated 6355 :mode nil :granularity nil :parent #190) #("As root configure the Guix profile\n" 0 35 (:parent #194))) (fixed-width (:begin 6391 :end 6427 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 6391 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6427 :end 6448 :contents-begin 6427 :contents-end 6447 :post-blank 1 :post-affiliated 6427 :mode nil :granularity nil :parent #190) #("and run for example\n" 0 20 (:parent #196))) (src-block (:language "bash" :switches nil :parameters nil :begin 6448 :end 6936 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mariadb && addgroup mariadb\nmkdir -p /export2/mariadb/database\nchown mariadb.mariadb -R /export2/mariadb/\nmkdir -p /var/run/mysqld\nchown mariadb.mariadb /var/run/mysqld\nsu mariadb\nmysql --version\n mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1\nmysql_install_db --user=mariadb --datadir=/export2/mariadb/database\nmysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #190)) (paragraph (:begin 6936 :end 6984 :contents-begin 6936 :contents-end 6983 :post-blank 1 :post-affiliated 6936 :mode nil :granularity nil :parent #190) #("If you want to run as root you may have to set\n" 0 47 (:parent #198))) (fixed-width (:begin 6984 :end 7024 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 6984 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7024 :end 7046 :contents-begin 7024 :contents-end 7045 :post-blank 1 :post-affiliated 7024 :mode nil :granularity nil :parent #190) #("You also need to set\n" 0 21 (:parent #200))) (fixed-width (:begin 7046 :end 7069 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 7046 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7069 :end 7149 :contents-begin 7069 :contents-end 7148 :post-blank 1 :post-affiliated 7069 :mode nil :granularity nil :parent #190) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #202))) (paragraph (:begin 7149 :end 7218 :contents-begin 7149 :contents-end 7217 :post-blank 1 :post-affiliated 7149 :mode nil :granularity nil :parent #190) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #203))) (fixed-width (:begin 7218 :end 7333 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 7218 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7333 :end 7411 :contents-begin 7333 :contents-end 7410 :post-blank 1 :post-affiliated 7333 :mode nil :granularity nil :parent #190) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #205))) (fixed-width (:begin 7411 :end 7521 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 7411 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7521 :end 7548 :contents-begin 7521 :contents-end 7547 :post-blank 1 :post-affiliated 7521 :mode nil :granularity nil :parent #190) #("When you get errors like:\n" 0 26 (:parent #207))) (fixed-width (:begin 7548 :end 7662 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 7548 :mode nil :granularity nil :parent #190)) (paragraph (:begin 7662 :end 7683 :contents-begin 7662 :contents-end 7682 :post-blank 1 :post-affiliated 7662 :mode nil :granularity nil :parent #190) #("you may need to set\n" 0 20 (:parent #209))) (fixed-width (:begin 7683 :end 7710 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 7683 :mode nil :granularity nil :parent #190)))) (headline (:raw-value "Load the small database in MySQL" :begin 7711 :end 9262 :pre-blank 1 :contents-begin 7748 :contents-end 9261 :robust-begin 7750 :robust-end 9259 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7711 :title (#("Load the small database in MySQL" 0 32 (:parent #188))) :parent #184 :cached t :org-element--cache-sync-key (1 . 7711) :granularity nil) (section (:begin 7748 :end 9262 :contents-begin 7748 :contents-end 9261 :robust-begin 7748 :robust-end 9259 :post-blank 1 :post-affiliated 7748 :mode section :granularity nil :parent #188) (paragraph (:begin 7748 :end 8055 :contents-begin 7748 :contents-end 8054 :post-blank 1 :post-affiliated 7748 :mode planning :granularity nil :parent #191) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #194)) (subscript (:begin 7911 :end 7918 :use-brackets-p nil :contents-begin 7912 :contents-end 7918 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 7918 :end 7920 :use-brackets-p nil :contents-begin 7919 :contents-end 7920 :post-blank 0 :parent #194) #("s" 0 1 (:parent #199))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #194)) (subscript (:begin 7996 :end 8003 :use-brackets-p nil :contents-begin 7997 :contents-end 8003 :post-blank 0 :parent #194) #("webqtl" 0 6 (:parent #201))) (subscript (:begin 8003 :end 8009 :use-brackets-p nil :contents-begin 8004 :contents-end 8009 :post-blank 0 :parent #194) #("plant" 0 5 (:parent #202))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #194))) (paragraph (:begin 8055 :end 8083 :contents-begin 8055 :contents-end 8082 :post-blank 1 :post-affiliated 8055 :mode nil :granularity nil :parent #191) #("Download one database from\n" 0 27 (:parent #195))) (paragraph (:begin 8083 :end 8164 :contents-begin 8083 :contents-end 8163 :post-blank 1 :post-affiliated 8083 :mode nil :granularity nil :parent #191) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 8083 :end 8162 :contents-begin nil :contents-end nil :post-blank 0 :parent #196)) #("\n" 0 1 (:parent #196))) (paragraph (:begin 8164 :end 8233 :contents-begin 8164 :contents-end 8232 :post-blank 1 :post-affiliated 8164 :mode nil :granularity nil :parent #191) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #197))) (src-block (:language "sh" :switches nil :parameters nil :begin 8233 :end 8375 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "cd ~/mysql\np7zip -d db_webqtl_s.7z\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*\n" :post-blank 1 :post-affiliated 8233 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8375 :end 8422 :contents-begin 8375 :contents-end 8421 :post-blank 1 :post-affiliated 8375 :mode nil :granularity nil :parent #191) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #199))) (fixed-width (:begin 8422 :end 8455 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 8422 :mode nil :granularity nil :parent #191)) (fixed-width (:begin 8455 :end 8472 :value "myslq -u root" :post-blank 2 :post-affiliated 8455 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8472 :end 8477 :contents-begin 8472 :contents-end 8476 :post-blank 1 :post-affiliated 8472 :mode nil :granularity nil :parent #191) #("and\n" 0 4 (:parent #202))) (fixed-width (:begin 8477 :end 8703 :value "mysql> show databases;\n+--------------------+\n| Database |\n+--------------------+\n| information_schema |\n| db_webqtl_s |\n| mysql |\n| performance_schema |\n+--------------------+" :post-blank 2 :post-affiliated 8477 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8703 :end 8768 :contents-begin 8703 :contents-end 8767 :post-blank 1 :post-affiliated 8703 :mode nil :granularity nil :parent #191) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #204))) (fixed-width (:begin 8768 :end 8859 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 8768 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8859 :end 8966 :contents-begin 8859 :contents-end 8965 :post-blank 1 :post-affiliated 8859 :mode nil :granularity nil :parent #191) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #206))) (paragraph (:begin 8966 :end 9129 :contents-begin 8966 :contents-end 9128 :post-blank 1 :post-affiliated 8966 :mode nil :granularity nil :parent #191) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #207))) (paragraph (:begin 9129 :end 9261 :contents-begin 9129 :contents-end 9261 :post-blank 0 :post-affiliated 9129 :mode nil :granularity nil :parent #191) #("Note for the plant database you can rename it to db" 0 51 (:parent #208)) (subscript (:begin 9180 :end 9187 :use-brackets-p nil :contents-begin 9181 :contents-end 9187 :post-blank 0 :parent #208) #("webqtl" 0 6 (:parent #212))) (subscript (:begin 9187 :end 9189 :use-brackets-p nil :contents-begin 9188 :contents-end 9189 :post-blank 0 :parent #208) #("s" 0 1 (:parent #213))) #(", or\nchange the settings in etc/default" 0 39 (:parent #208)) (subscript (:begin 9228 :end 9241 :use-brackets-p nil :contents-begin 9229 :contents-end 9240 :post-blank 1 :parent #208) #("settings.py" 0 11 (:parent #215))) #("to match your path.\n" 0 20 (:parent #208)))))) (headline (:raw-value "Get genotype files" :begin 9262 :end 9504 :pre-blank 1 :contents-begin 9284 :contents-end 9503 :robust-begin 9286 :robust-end 9501 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9262 :title (#("Get genotype files" 0 18 (:parent #185))) :parent #172 :cached t :org-element--cache-sync-key (2 . 9262) :granularity nil) (section (:begin 9284 :end 9504 :contents-begin 9284 :contents-end 9503 :robust-begin 9284 :robust-end 9501 :post-blank 1 :post-affiliated 9284 :mode section :granularity nil :parent #185) (paragraph (:begin 9284 :end 9423 :contents-begin 9284 :contents-end 9422 :post-blank 1 :post-affiliated 9284 :mode planning :granularity nil :parent #188) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #191)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 9342 :end 9421 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #("\n" 0 1 (:parent #191))) (src-block (:language "sh" :switches nil :parameters nil :begin 9423 :end 9503 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "mkdir -p $HOME/genotype_files\ncd $HOME/genotype_files\n\n" :post-blank 0 :post-affiliated 9423 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "GN2 Dependency Graph" :begin 9504 :end 9668 :pre-blank 1 :contents-begin 9528 :contents-end 9667 :robust-begin 9530 :robust-end 9665 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9504 :title (#("GN2 Dependency Graph" 0 20 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 9528 :end 9668 :contents-begin 9528 :contents-end 9667 :robust-begin 9528 :robust-end 9665 :post-blank 1 :post-affiliated 9528 :mode section :granularity nil :parent #186) (paragraph (:begin 9528 :end 9589 :contents-begin 9528 :contents-end 9588 :post-blank 1 :post-affiliated 9528 :mode planning :granularity nil :parent #189) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #192))) (paragraph (:begin 9589 :end 9667 :contents-begin 9619 :contents-end 9667 :post-blank 0 :post-affiliated 9619 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #189) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 9619 :end 9666 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))))) (headline (:raw-value "Working with the GN2 source code" :begin 9668 :end 9730 :pre-blank 1 :contents-begin 9704 :contents-end 9729 :robust-begin 9706 :robust-end 9727 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9668 :title (#("Working with the GN2 source code" 0 32 (:parent #187))) :mode nil :granularity nil :parent #172) (section (:begin 9704 :end 9730 :contents-begin 9704 :contents-end 9729 :robust-begin 9704 :robust-end 9727 :post-blank 1 :post-affiliated 9704 :mode section :granularity nil :parent #187) (paragraph (:begin 9704 :end 9729 :contents-begin 9704 :contents-end 9729 :post-blank 0 :post-affiliated 9704 :mode planning :granularity nil :parent #190) #("See " 0 4 (:parent #193)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 9708 :end 9727 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #(".\n" 0 2 (:parent #193))))) (headline (:raw-value "Read more" :begin 9730 :end 9880 :pre-blank 1 :contents-begin 9743 :contents-end 9879 :robust-begin 9745 :robust-end 9877 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9730 :title (#("Read more" 0 9 (:parent #188))) :mode nil :granularity nil :parent #172) (section (:begin 9743 :end 9880 :contents-begin 9743 :contents-end 9879 :robust-begin 9743 :robust-end 9877 :post-blank 1 :post-affiliated 9743 :mode section :granularity nil :parent #188) (paragraph (:begin 9743 :end 9879 :contents-begin 9743 :contents-end 9879 :post-blank 0 :post-affiliated 9743 :mode planning :granularity nil :parent #191) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #194)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 9798 :end 9818 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #194))))) (headline (:raw-value "Trouble shooting" :begin 9880 :end 12330 :pre-blank 1 :contents-begin 9900 :contents-end 12329 :robust-begin 9902 :robust-end 12327 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9880 :title (#("Trouble shooting" 0 16 (:parent #189))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 9900 :end 10434 :pre-blank 1 :contents-begin 9940 :contents-end 10434 :robust-begin 9942 :robust-end 10432 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9900 :title (#("ImportError: No module named jinja2" 0 35 (:parent #192))) :mode section :granularity nil :parent #189) (section (:begin 9940 :end 10434 :contents-begin 9940 :contents-end 10434 :robust-begin 9940 :robust-end 10432 :post-blank 0 :post-affiliated 9940 :mode section :granularity nil :parent #192) (paragraph (:begin 9940 :end 10175 :contents-begin 9940 :contents-end 10174 :post-blank 1 :post-affiliated 9940 :mode planning :granularity nil :parent #195) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #198)) (subscript (:begin 10107 :end 10113 :use-brackets-p nil :contents-begin 10108 :contents-end 10112 :post-blank 1 :parent #198) #("PATH" 0 4 (:parent #202))) #("and R" 0 5 (:parent #198)) (subscript (:begin 10118 :end 10123 :use-brackets-p nil :contents-begin 10119 :contents-end 10123 :post-blank 0 :parent #198) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 10123 :end 10129 :use-brackets-p nil :contents-begin 10124 :contents-end 10128 :post-blank 1 :parent #198) #("SITE" 0 4 (:parent #205))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #198))) (fixed-width (:begin 10175 :end 10206 :value "guix package --search-paths" :post-blank 2 :post-affiliated 10175 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10206 :end 10222 :contents-begin 10206 :contents-end 10221 :post-blank 1 :post-affiliated 10206 :mode nil :granularity nil :parent #195) #("On one system:\n" 0 15 (:parent #200))) (fixed-width (:begin 10222 :end 10410 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python3.8/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 10222 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10410 :end 10434 :contents-begin 10410 :contents-end 10434 :post-blank 0 :post-affiliated 10410 :mode nil :granularity nil :parent #195) #("and perhaps a few more.\n" 0 24 (:parent #202))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 10434 :end 10930 :pre-blank 1 :contents-begin 10543 :contents-end 10929 :robust-begin 10545 :robust-end 10927 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 10434 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #193)) (subscript (:begin 10477 :end 10482 :use-brackets-p nil :contents-begin 10478 :contents-end 10482 :post-blank 0 :parent #193) #("data" 0 4 (:parent #235))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #193)) (subscript (:begin 10525 :end 10531 :use-brackets-p nil :contents-begin 10526 :contents-end 10531 :post-blank 0 :parent #193) #("files" 0 5 (:parent #237))) #("/genotype'" 0 10 (:parent #193))) :mode nil :granularity nil :parent #189) (section (:begin 10543 :end 10930 :contents-begin 10543 :contents-end 10929 :robust-begin 10543 :robust-end 10927 :post-blank 1 :post-affiliated 10543 :mode section :granularity nil :parent #193) (paragraph (:begin 10543 :end 10765 :contents-begin 10543 :contents-end 10764 :post-blank 1 :post-affiliated 10543 :mode planning :granularity nil :parent #196) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #199)) (subscript (:begin 10592 :end 10597 :use-brackets-p nil :contents-begin 10593 :contents-end 10597 :post-blank 0 :parent #199) #("data" 0 4 (:parent #203))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #199)) (subscript (:begin 10721 :end 10734 :use-brackets-p nil :contents-begin 10722 :contents-end 10733 :post-blank 1 :parent #199) #("settings.py" 0 11 (:parent #205))) #("(see above in\nthis document).\n" 0 30 (:parent #199))) (paragraph (:begin 10765 :end 10839 :contents-begin 10765 :contents-end 10838 :post-blank 1 :post-affiliated 10765 :mode nil :granularity nil :parent #196) #("You can use the GENENETWORK" 0 27 (:parent #200)) (subscript (:begin 10792 :end 10799 :use-brackets-p nil :contents-begin 10793 :contents-end 10798 :post-blank 1 :parent #200) #("FILES" 0 5 (:parent #204))) #("switch to set the datadir, for example\n" 0 39 (:parent #200))) (fixed-width (:begin 10839 :end 10929 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 10839 :mode nil :granularity nil :parent #196)))) (headline (:raw-value "Can't run a module" :begin 10930 :end 11164 :pre-blank 1 :contents-begin 10953 :contents-end 11164 :robust-begin 10955 :robust-end 11162 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 10930 :title (#("Can't run a module" 0 18 (:parent #194))) :mode nil :granularity nil :parent #189) (section (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :robust-begin 10953 :robust-end 11162 :post-blank 0 :post-affiliated 10953 :mode section :granularity nil :parent #194) (paragraph (:begin 10953 :end 11164 :contents-begin 10953 :contents-end 11164 :post-blank 0 :post-affiliated 10953 :mode planning :granularity nil :parent #197) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #200))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 11164 :end 11665 :pre-blank 1 :contents-begin 11196 :contents-end 11664 :robust-begin 11198 :robust-end 11662 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 11164 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #195))) :mode nil :granularity nil :parent #189) (section (:begin 11196 :end 11665 :contents-begin 11196 :contents-end 11664 :robust-begin 11196 :robust-end 11662 :post-blank 1 :post-affiliated 11196 :mode section :granularity nil :parent #195) (paragraph (:begin 11196 :end 11208 :contents-begin 11196 :contents-end 11207 :post-blank 1 :post-affiliated 11196 :mode planning :granularity nil :parent #198) #("This error\n" 0 11 (:parent #201))) (fixed-width (:begin 11208 :end 11288 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 11208 :mode nil :granularity nil :parent #198)) (paragraph (:begin 11288 :end 11419 :contents-begin 11288 :contents-end 11418 :post-blank 1 :post-affiliated 11288 :mode nil :granularity nil :parent #198) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #203))) (paragraph (:begin 11419 :end 11664 :contents-begin 11419 :contents-end 11664 :post-blank 0 :post-affiliated 11419 :mode nil :granularity nil :parent #198) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #204)) (subscript (:begin 11482 :end 11487 :use-brackets-p nil :contents-begin 11483 :contents-end 11487 :post-blank 0 :parent #204) #("LIBS" 0 4 (:parent #208))) (subscript (:begin 11487 :end 11492 :use-brackets-p nil :contents-begin 11488 :contents-end 11492 :post-blank 0 :parent #204) #("SITE" 0 4 (:parent #209))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #204))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 11665 :end 12330 :pre-blank 1 :contents-begin 11717 :contents-end 12329 :robust-begin 11719 :robust-end 12327 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 11665 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #196))) :mode nil :granularity nil :parent #189) (section (:begin 11717 :end 12330 :contents-begin 11717 :contents-end 12329 :robust-begin 11717 :robust-end 12327 :post-blank 1 :post-affiliated 11717 :mode section :granularity nil :parent #196) (paragraph (:begin 11717 :end 11738 :contents-begin 11717 :contents-end 11737 :post-blank 1 :post-affiliated 11717 :mode planning :granularity nil :parent #199) #("The following error\n" 0 20 (:parent #202))) (fixed-width (:begin 11738 :end 11933 :value "sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\\'t connect to local MySQL server through socket \\'/run/mysqld/mysqld.sock\\' (2 \"No such file or directory\")')" :post-blank 2 :post-affiliated 11738 :mode nil :granularity nil :parent #199)) (paragraph (:begin 11933 :end 12091 :contents-begin 11933 :contents-end 12090 :post-blank 1 :post-affiliated 11933 :mode nil :granularity nil :parent #199) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #204))) (fixed-width (:begin 12091 :end 12113 :value "mysql -h localhost" :post-blank 2 :post-affiliated 12091 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12113 :end 12170 :contents-begin 12113 :contents-end 12169 :post-blank 1 :post-affiliated 12113 :mode nil :granularity nil :parent #199) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #206))) (fixed-width (:begin 12170 :end 12192 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 12170 :mode nil :granularity nil :parent #199)) (paragraph (:begin 12192 :end 12263 :contents-begin 12192 :contents-end 12262 :post-blank 1 :post-affiliated 12192 :mode nil :granularity nil :parent #199) #("if that works run genenetwork after setting SQL" 0 47 (:parent #208)) (subscript (:begin 12239 :end 12244 :use-brackets-p nil :contents-begin 12240 :contents-end 12243 :post-blank 1 :parent #208) #("URI" 0 3 (:parent #212))) #("to something like\n" 0 18 (:parent #208))) (fixed-width (:begin 12263 :end 12329 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 12263 :mode nil :granularity nil :parent #199))))) (headline (:raw-value "NOTES" :begin 12330 :end 13242 :pre-blank 1 :contents-begin 12339 :contents-end 13242 :robust-begin 12341 :robust-end 13240 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 12330 :title (#("NOTES" 0 5 (:parent #190))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Deploying GN2 official" :begin 12339 :end 13242 :pre-blank 1 :contents-begin 12366 :contents-end 13242 :robust-begin 12368 :robust-end 13240 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 0 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 12339 :title (#("Deploying GN2 official" 0 22 (:parent #193))) :mode section :granularity nil :parent #190) (section (:begin 12366 :end 13242 :contents-begin 12366 :contents-end 13242 :robust-begin 12366 :robust-end 13240 :post-blank 0 :post-affiliated 12366 :mode section :granularity nil :parent #193) (paragraph (:begin 12366 :end 12422 :contents-begin 12366 :contents-end 12421 :post-blank 1 :post-affiliated 12366 :mode planning :granularity nil :parent #196) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #199))) (plain-list (:type unordered :begin 12422 :end 13242 :contents-begin 12422 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12422 :mode nil :granularity nil :parent #196) (item (:bullet "- " :begin 12422 :end 13242 :contents-begin 12428 :contents-end 13242 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12422 :tag nil :mode item :granularity nil :parent #200) (paragraph (:begin 12428 :end 12441 :contents-begin 12428 :contents-end 12441 :post-blank 0 :post-affiliated 12428 :mode nil :granularity nil :parent #203) #("Base install\n" 0 13 (:parent #206))) (plain-list (:type unordered :begin 12441 :end 13242 :contents-begin 12441 :contents-end 13242 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12441 :mode nil :granularity nil :parent #203) (item (:bullet "+ " :begin 12441 :end 12502 :contents-begin 12449 :contents-end 12502 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12441 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12449 :end 12502 :contents-begin 12449 :contents-end 12502 :post-blank 0 :post-affiliated 12449 :mode nil :granularity nil :parent #210) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #213)))) (item (:bullet "+ " :begin 12502 :end 12780 :contents-begin 12510 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12502 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12510 :end 12531 :contents-begin 12510 :contents-end 12531 :post-blank 0 :post-affiliated 12510 :mode nil :granularity nil :parent #211) #("Get Guix build going\n" 0 21 (:parent #214))) (plain-list (:type unordered :begin 12531 :end 12780 :contents-begin 12531 :contents-end 12780 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12531 :mode nil :granularity nil :parent #211) (item (:bullet "- " :begin 12531 :end 12575 :contents-begin 12541 :contents-end 12575 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12531 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12541 :end 12575 :contents-begin 12541 :contents-end 12575 :post-blank 0 :post-affiliated 12541 :mode nil :granularity nil :parent #218) #("Build the correct version of Guix\n" 0 34 (:parent #221)))) (item (:bullet "- " :begin 12575 :end 12702 :contents-begin 12585 :contents-end 12702 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12575 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12585 :end 12702 :contents-begin 12585 :contents-end 12702 :post-blank 0 :post-affiliated 12585 :mode nil :granularity nil :parent #219) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #222)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 12648 :end 12701 :contents-begin nil :contents-end nil :post-blank 0 :parent #222)) #("\n" 0 1 (:parent #222)))) (item (:bullet "- " :begin 12702 :end 12780 :contents-begin 12712 :contents-end 12780 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12702 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 12712 :end 12780 :contents-begin 12712 :contents-end 12780 :post-blank 0 :post-affiliated 12712 :mode nil :granularity nil :parent #220) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #223)))))) (item (:bullet "+ " :begin 12780 :end 12826 :contents-begin 12788 :contents-end 12826 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12780 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12788 :end 12826 :contents-begin 12788 :contents-end 12826 :post-blank 0 :post-affiliated 12788 :mode nil :granularity nil :parent #212) #("Create a gn2 user and home with space\n" 0 38 (:parent #215)))) (item (:bullet "+ " :begin 12826 :end 12926 :contents-begin 12834 :contents-end 12926 :checkbox off :counter nil :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :pre-blank 0 :post-blank 0 :post-affiliated 12826 :tag nil :mode item :granularity nil :parent #207) (paragraph (:begin 12834 :end 12848 :contents-begin 12834 :contents-end 12848 :post-blank 0 :post-affiliated 12834 :mode nil :granularity nil :parent #213) #("Install redis\n" 0 14 (:parent #216))) (plain-list (:type unordered :begin 12848 :end 12926 :contents-begin 12848 :contents-end 12926 :structure ((12422 0 "- " nil "[ ]" nil 13242) (12441 2 "+ " nil "[ ]" nil 12502) (12502 2 "+ " nil "[ ]" nil 12780) (12531 4 "- " nil "[ ]" nil 12575) (12575 4 "- " nil "[ ]" nil 12702) (12702 4 "- " nil "[ ]" nil 12780) (12780 2 "+ " nil "[ ]" nil 12826) (12826 2 "+ " nil "[ ]" nil 12926) (12848 4 "- " nil "[ ]" nil 12873) (12873 4 "- " nil "[ ]" nil 12900) (12900 4 "- " nil "[ ]" nil 12926) (12926 2 "+ " nil "[ ]" nil 13151) (12984 4 "- " nil "[ ]" nil 13009) (13009 4 "- " nil "[ ]" nil 13037) (13037 4 "- " nil "[ ]" nil 13064) (13064 4 "- " nil "[ ]" nil 13128) (13128 4 "- " nil "[ ]" nil 13151) (13151 2 "+ " nil "[ ]" nil 13167) (13167 2 "+ " nil "[ ]" nil 13188) (13188 2 "+ " nil "[ ]" nil 13242) (13217 4 "- " nil "[ ]" nil 13242)) :post-blank 0 :post-affiliated 12848 :mode nil :granularity nil :parent #213) (item (:bullet "- " :begin 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