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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 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :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 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :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 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :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 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :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 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #178) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #181) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #184)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #184)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #184))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #179) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #182) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #185)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #189) #("settings.py" 0 11 (:parent #193)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #185))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #182) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #187))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #182) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #189))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #180) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #183) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #186)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #186) #("README" 0 6 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #181) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #184) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #187))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #182))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #185))) :mode section :granularity nil :parent #182) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #185) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #188) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #191))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #188) #("As root configure the Guix profile\n" 0 35 (:parent #192))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #188)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #188) #("and run for example\n" 0 20 (:parent #194))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #188)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #188) #("If you want to run as root you may have to set\n" 0 47 (:parent #196))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #188) #("You also need to set\n" 0 21 (:parent #198))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #188) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #200))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #188) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #201))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #188) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #203))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #188) #("When you get errors like:\n" 0 26 (:parent #205))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #188) #("you may need to set\n" 0 20 (:parent #207))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #186))) :mode nil :granularity nil :parent #182) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #186) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #189) #("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 #192)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #192) #("webqtl" 0 6 (:parent #196))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #192) #("s" 0 1 (:parent #197))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #192)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #192) #("webqtl" 0 6 (:parent #199))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #192) #("plant" 0 5 (:parent #200))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #192))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #189) #("Download one database from\n" 0 27 (:parent #193))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #189) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #189) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #195))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #189) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #189)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #189) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #189) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #189) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #189) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #189) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #206) #("webqtl" 0 6 (:parent #210))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #206) #("s" 0 1 (:parent #211))) #(", or\nchange the settings in etc/default" 0 39 (:parent #206)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #206) #("settings.py" 0 11 (:parent #213))) #("to match your path.\n" 0 20 (:parent #206)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #183) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #186) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #189)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #184) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #187) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #190))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #187) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #("\n" 0 1 (:parent #191))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #185) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #188) #("See " 0 4 (:parent #191)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #(".\n" 0 2 (:parent #191))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #186) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #189) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #192)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #192))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #187))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #190))) :mode section :granularity nil :parent #187) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #190) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #193) #("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 #196)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #196) #("PATH" 0 4 (:parent #200))) #("and R" 0 5 (:parent #196)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #196) #("LIBS" 0 4 (:parent #202))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #196) #("SITE" 0 4 (:parent #203))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #196))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #193) #("On one system:\n" 0 15 (:parent #198))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #193) #("and perhaps a few more.\n" 0 24 (:parent #200))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #191)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #191) #("data" 0 4 (:parent #233))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #191)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #191) #("files" 0 5 (:parent #235))) #("/genotype'" 0 10 (:parent #191))) :mode nil :granularity nil :parent #187) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #191) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #194) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #197)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #197) #("data" 0 4 (:parent #201))) #(". 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 #197)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #197) #("settings.py" 0 11 (:parent #203))) #("(see above in\nthis document).\n" 0 30 (:parent #197))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #194) #("You can use the GENENETWORK" 0 27 (:parent #198)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #198) #("FILES" 0 5 (:parent #202))) #("switch to set the datadir, for example\n" 0 39 (:parent #198))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #194)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #192))) :mode nil :granularity nil :parent #187) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #192) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #195) #("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 #198))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #193))) :mode nil :granularity nil :parent #187) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #193) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #196) #("This error\n" 0 11 (:parent #199))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #196)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #196) #("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 #201))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #196) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #202)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #202) #("LIBS" 0 4 (:parent #206))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #202) #("SITE" 0 4 (:parent #207))) #(". 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 #202))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #194))) :mode nil :granularity nil :parent #187) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #194) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #197) #("The following error\n" 0 20 (:parent #200))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #197)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #197) #("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 #202))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #197)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #197) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #204))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #197)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #197) #("if that works run genenetwork after setting SQL" 0 47 (:parent #206)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #206) #("URI" 0 3 (:parent #210))) #("to something like\n" 0 18 (:parent #206))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #197))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #188))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #191))) :mode section :granularity nil :parent #188) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #191) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #194) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #197))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #201) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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"http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #220)) #("\n" 0 1 (:parent #220)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #213) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #218) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #221)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #205) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #210) #("Create a gn2 user and home with space\n" 0 38 (:parent #213)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 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4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #215) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #218) #("add to systemd\n" 0 15 (:parent #221)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 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:post-affiliated 9994 :mode nil :granularity nil :parent #212) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #215))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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:contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #343) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #367) #("Base install\n" 0 13 (:parent #370))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #374) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #377)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #375) #("Get Guix build going\n" 0 21 (:parent #378))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #375) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #379) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #382) #("Build the correct version of Guix\n" 0 34 (:parent #385)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #379) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #383) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #386)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #386)) #("\n" 0 1 (:parent #386)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #379) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #384) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #387)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #376) #("Create a gn2 user and home with space\n" 0 38 (:parent #379)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #377) #("Install redis\n" 0 14 (:parent #380))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #377) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #381) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #384) #("add to systemd\n" 0 15 (:parent #387)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 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 #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 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :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 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :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 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :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 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :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 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #178) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #181) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #184)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #184)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #184))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #179) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #182) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #185)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #189) #("settings.py" 0 11 (:parent #193)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #185))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #182) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #187))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #182)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #182) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #189))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #180))) :mode nil :granularity nil :parent #172) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #180) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #183) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #186)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #186) #("README" 0 6 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #181) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #184) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #187))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #182))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #185))) :mode section :granularity nil :parent #182) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #185) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #188) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #191))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #188) #("As root configure the Guix profile\n" 0 35 (:parent #192))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #188)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #188) #("and run for example\n" 0 20 (:parent #194))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #188)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #188) #("If you want to run as root you may have to set\n" 0 47 (:parent #196))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #188) #("You also need to set\n" 0 21 (:parent #198))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #188) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #200))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #188) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #201))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #188) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #203))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #188) #("When you get errors like:\n" 0 26 (:parent #205))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #188)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #188) #("you may need to set\n" 0 20 (:parent #207))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #188)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #186))) :mode nil :granularity nil :parent #182) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #186) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #189) #("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 #192)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #192) #("webqtl" 0 6 (:parent #196))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #192) #("s" 0 1 (:parent #197))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #192)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #192) #("webqtl" 0 6 (:parent #199))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #192) #("plant" 0 5 (:parent #200))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #192))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #189) #("Download one database from\n" 0 27 (:parent #193))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #189) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #189) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #195))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #189) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #189)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #189) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #189) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #189)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #189) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #189) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #189) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #206) #("webqtl" 0 6 (:parent #210))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #206) #("s" 0 1 (:parent #211))) #(", or\nchange the settings in etc/default" 0 39 (:parent #206)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #206) #("settings.py" 0 11 (:parent #213))) #("to match your path.\n" 0 20 (:parent #206)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #183))) :mode nil :granularity nil :parent #172) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #183) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #186) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #189)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #184) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #187) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #190))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #187) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #("\n" 0 1 (:parent #191))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #185) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #188) #("See " 0 4 (:parent #191)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #(".\n" 0 2 (:parent #191))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #186) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #189) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #192)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #192))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #187))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #190))) :mode section :granularity nil :parent #187) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #190) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #193) #("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 #196)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #196) #("PATH" 0 4 (:parent #200))) #("and R" 0 5 (:parent #196)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #196) #("LIBS" 0 4 (:parent #202))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #196) #("SITE" 0 4 (:parent #203))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #196))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #193) #("On one system:\n" 0 15 (:parent #198))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #193) #("and perhaps a few more.\n" 0 24 (:parent #200))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #191)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #191) #("data" 0 4 (:parent #233))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #191)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #191) #("files" 0 5 (:parent #235))) #("/genotype'" 0 10 (:parent #191))) :mode nil :granularity nil :parent #187) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #191) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #194) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #197)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #197) #("data" 0 4 (:parent #201))) #(". 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 #197)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #197) #("settings.py" 0 11 (:parent #203))) #("(see above in\nthis document).\n" 0 30 (:parent #197))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #194) #("You can use the GENENETWORK" 0 27 (:parent #198)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #198) #("FILES" 0 5 (:parent #202))) #("switch to set the datadir, for example\n" 0 39 (:parent #198))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #194)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #192))) :mode nil :granularity nil :parent #187) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #192) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #195) #("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 #198))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #193))) :mode nil :granularity nil :parent #187) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #193) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #196) #("This error\n" 0 11 (:parent #199))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #196)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #196) #("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 #201))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #196) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #202)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #202) #("LIBS" 0 4 (:parent #206))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #202) #("SITE" 0 4 (:parent #207))) #(". 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 #202))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #194))) :mode nil :granularity nil :parent #187) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #194) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #197) #("The following error\n" 0 20 (:parent #200))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #197)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #197) #("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 #202))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #197)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #197) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #204))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #197)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #197) #("if that works run genenetwork after setting SQL" 0 47 (:parent #206)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #206) #("URI" 0 3 (:parent #210))) #("to something like\n" 0 18 (:parent #206))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #197))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #188))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #191))) :mode section :granularity nil :parent #188) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #191) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #194) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #197))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #194) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #198) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #201) #("Base install\n" 0 13 (:parent #204))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #201) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #205) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #208) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #211)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #205) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #209) #("Get Guix build going\n" 0 21 (:parent #212))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #184)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #184) #("Guix-notes" 0 10 (:parent #190))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #184))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #181) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #185) #("Guix bioinformatics" 0 19 (:parent #189))) #("and " 0 4 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #185) #("GNU Guix" 0 8 (:parent #191))) #(".\n" 0 2 (:parent #185))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #181) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #186)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #186) #("GN2 Dependency Graph" 0 20 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #179))) :mode nil :granularity nil :parent #173) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #179) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :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 2325 :end 2363 :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.\n" 0 82 (:parent #185))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #180))) :mode nil :granularity nil :parent #173) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #180) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #183) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #186)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #186) #("default" 0 7 (:parent #190)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #190) #("settings.py" 0 11 (:parent #194)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #186))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #183)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #183) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #188))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #183)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #183) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #190))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #181))) :mode nil :granularity nil :parent #173) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #181) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #184) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #187)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #187) #("README" 0 6 (:parent #191))) #(".\n" 0 2 (:parent #187))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #182))) :mode nil :granularity nil :parent #173) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #182) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 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(:parent #186))) :mode section :granularity nil :parent #183) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #186) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #189) #("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 #192))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #189) #("As root configure the Guix profile\n" 0 35 (:parent #193))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #189)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #189) #("and run for example\n" 0 20 (:parent #195))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #189)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #189) #("If you want to run as root you may have to set\n" 0 47 (:parent #197))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #189)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #189) #("You also need to set\n" 0 21 (:parent #199))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #189)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #189) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #201))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #189) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #202))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #189)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #189) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #204))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #189)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #189) #("When you get errors like:\n" 0 26 (:parent #206))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #189)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #189) #("you may need to set\n" 0 20 (:parent #208))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #189)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #187))) :mode nil :granularity nil :parent #183) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #187) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #190) #("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 #193)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #193) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #193) #("s" 0 1 (:parent #198))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #193)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #193) #("webqtl" 0 6 (:parent #200))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #193) #("plant" 0 5 (:parent #201))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #193))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #190) #("Download one database from\n" 0 27 (:parent #194))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #190) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #195)) #("\n" 0 1 (:parent #195))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #190) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #196))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #190)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #190) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #198))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #190)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #190)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #190) #("and\n" 0 4 (:parent #201))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #190)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #190) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #203))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #190)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #190) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #205))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #190) #("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 #206))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #190) #("Note for the plant database you can rename it to db" 0 51 (:parent #207)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #207) #("webqtl" 0 6 (:parent #211))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #207) #("s" 0 1 (:parent #212))) #(", or\nchange the settings in etc/default" 0 39 (:parent #207)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #207) #("settings.py" 0 11 (:parent #214))) #("to match your path.\n" 0 20 (:parent #207)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #184))) :mode nil :granularity nil :parent #173) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #184) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #187) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #190)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #("\n" 0 1 (:parent #190))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #187)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #185))) :mode nil :granularity nil :parent #173) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #185) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #188) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #191))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #188) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #186))) :mode nil :granularity nil :parent #173) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #186) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #189) #("See " 0 4 (:parent #192)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #(".\n" 0 2 (:parent #192))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #187))) :mode nil :granularity nil :parent #173) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #187) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #190) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #193)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #193))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #188))) :mode nil :granularity nil :parent #173) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #191))) :mode section :granularity nil :parent #188) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #191) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #194) #("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 #197)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #197) #("PATH" 0 4 (:parent #201))) #("and R" 0 5 (:parent #197)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #197) #("LIBS" 0 4 (:parent #203))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #197) #("SITE" 0 4 (:parent #204))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #197))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #194)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #194) #("On one system:\n" 0 15 (:parent #199))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #194)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #194) #("and perhaps a few more.\n" 0 24 (:parent #201))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #192)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #192) #("data" 0 4 (:parent #234))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #192)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #192) #("files" 0 5 (:parent #236))) #("/genotype'" 0 10 (:parent #192))) :mode nil :granularity nil :parent #188) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #192) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #195) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #198)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #198) #("data" 0 4 (:parent #202))) #(". 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 #198)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #198) #("settings.py" 0 11 (:parent #204))) #("(see above in\nthis document).\n" 0 30 (:parent #198))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #195) #("You can use the GENENETWORK" 0 27 (:parent #199)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #199) #("FILES" 0 5 (:parent #203))) #("switch to set the datadir, for example\n" 0 39 (:parent #199))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #195)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #193))) :mode nil :granularity nil :parent #188) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #193) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #196) #("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 #199))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #194))) :mode nil :granularity nil :parent #188) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #194) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #197) #("This error\n" 0 11 (:parent #200))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #197)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #197) #("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 #202))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #197) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #203)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #203) #("LIBS" 0 4 (:parent #207))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #203) #("SITE" 0 4 (:parent #208))) #(". 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 #203))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #195))) :mode nil :granularity nil :parent #188) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #195) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #198) #("The following error\n" 0 20 (:parent #201))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #198)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #198) #("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 #203))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #198)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #198) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #205))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #198)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #198) #("if that works run genenetwork after setting SQL" 0 47 (:parent #207)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #207) #("URI" 0 3 (:parent #211))) #("to something like\n" 0 18 (:parent #207))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #198))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #189))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #192))) :mode section :granularity nil :parent #189) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #192) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #195) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #198))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #195) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #199) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #202) #("Base install\n" 0 13 (:parent #205))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #202) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #206) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #209) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #212)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #206) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #210) #("Get Guix build going\n" 0 21 (:parent #213))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #210) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #214) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #217) #("Build the correct version of Guix\n" 0 34 (:parent #220)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #214) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #218) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #221)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #221)) #("\n" 0 1 (:parent #221)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #214) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #219) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #222)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #206) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #211) #("Create a gn2 user and home with space\n" 0 38 (:parent #214)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #206) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #212) #("Install redis\n" 0 14 (:parent #215))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #212) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #216) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #219) #("add to systemd\n" 0 15 (:parent #222)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 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#154))) #105 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #156) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #159) #("Large system deployments can get very " 0 38 (:parent #162)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #162) #("complex" 0 7 (:parent #166))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #162) #("Guix-notes" 0 10 (:parent #168))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #162))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #159) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #163) #("Guix bioinformatics" 0 19 (:parent #167))) #("and " 0 4 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #163) #("GNU Guix" 0 8 (:parent #169))) #(".\n" 0 2 (:parent #163))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #159) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #164)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #164) #("GN2 Dependency Graph" 0 20 (:parent #168))) #(".\n" 0 2 (:parent #164))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #157) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #160) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #163)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #163)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #163))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #158) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #161) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #164)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #164) #("default" 0 7 (:parent #168)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #168) #("settings.py" 0 11 (:parent #172)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #164))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #161)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #161) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #166))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #161)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #161) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #168))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #159))) :mode nil :granularity nil :parent #151) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #159) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #162) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #165)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #165) #("README" 0 6 (:parent #169))) #(".\n" 0 2 (:parent #165))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #160))) :mode nil :granularity nil :parent #151) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #160) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #163) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #166))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #161))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #164))) :mode section :granularity nil :parent #161) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #164) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #167) #("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 #170))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #167) #("As root configure the Guix profile\n" 0 35 (:parent #171))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #167)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #167) #("and run for example\n" 0 20 (:parent #173))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #167)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #167) #("If you want to run as root you may have to set\n" 0 47 (:parent #175))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #167)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #167) #("You also need to set\n" 0 21 (:parent #177))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #167)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #167) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #179))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #167) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #180))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #167)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #167) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #182))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #167)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #167) #("When you get errors like:\n" 0 26 (:parent #184))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #167)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #167) #("you may need to set\n" 0 20 (:parent #186))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #167)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #165))) :mode nil :granularity nil :parent #161) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #165) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #168) #("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 #171)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #171) #("webqtl" 0 6 (:parent #175))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #171) #("s" 0 1 (:parent #176))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #171)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #171) #("webqtl" 0 6 (:parent #178))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #171) #("plant" 0 5 (:parent #179))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #171))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #168) #("Download one database from\n" 0 27 (:parent #172))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #168) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #173)) #("\n" 0 1 (:parent #173))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #168) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #174))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #168)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #168) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #176))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #168)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #168)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #168) #("and\n" 0 4 (:parent #179))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #168)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #168) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #181))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #168)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #168) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #183))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #168) #("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 #184))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #168) #("Note for the plant database you can rename it to db" 0 51 (:parent #185)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #185) #("webqtl" 0 6 (:parent #189))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #185) #("s" 0 1 (:parent #190))) #(", or\nchange the settings in etc/default" 0 39 (:parent #185)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #185) #("settings.py" 0 11 (:parent #192))) #("to match your path.\n" 0 20 (:parent #185)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #162))) :mode nil :granularity nil :parent #151) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #162) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #165) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #168)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\n" 0 1 (:parent #168))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #163))) :mode nil :granularity nil :parent #151) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #163) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #166) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #169))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #166) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #("\n" 0 1 (:parent #170))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #164))) :mode nil :granularity nil :parent #151) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #164) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #167) #("See " 0 4 (:parent #170)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #170)) #(".\n" 0 2 (:parent #170))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #165))) :mode nil :granularity nil :parent #151) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #165) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #168) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #171)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #171)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #171))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #166))) :mode nil :granularity nil :parent #151) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #169))) :mode section :granularity nil :parent #166) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #169) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #172) #("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 #175)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #175) #("PATH" 0 4 (:parent #179))) #("and R" 0 5 (:parent #175)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #175) #("LIBS" 0 4 (:parent #181))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #175) #("SITE" 0 4 (:parent #182))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #175))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #172)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #172) #("On one system:\n" 0 15 (:parent #177))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #172)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #172) #("and perhaps a few more.\n" 0 24 (:parent #179))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #170)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #170) #("data" 0 4 (:parent #212))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #170)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #170) #("files" 0 5 (:parent #214))) #("/genotype'" 0 10 (:parent #170))) :mode nil :granularity nil :parent #166) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #170) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #173) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #176)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #176) #("data" 0 4 (:parent #180))) #(". 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 #176)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #176) #("settings.py" 0 11 (:parent #182))) #("(see above in\nthis document).\n" 0 30 (:parent #176))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #173) #("You can use the GENENETWORK" 0 27 (:parent #177)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #177) #("FILES" 0 5 (:parent #181))) #("switch to set the datadir, for example\n" 0 39 (:parent #177))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #173)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #171))) :mode nil :granularity nil :parent #166) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #171) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #174) #("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 #177))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #172))) :mode nil :granularity nil :parent #166) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #172) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #175) #("This error\n" 0 11 (:parent #178))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #175)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #175) #("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 #180))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #175) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #181)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #181) #("LIBS" 0 4 (:parent #185))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #181) #("SITE" 0 4 (:parent #186))) #(". 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 #181))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #173))) :mode nil :granularity nil :parent #166) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #173) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #176) #("The following error\n" 0 20 (:parent #179))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #176)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #176) #("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 #181))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #176)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #176) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #183))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #176)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #176) #("if that works run genenetwork after setting SQL" 0 47 (:parent #185)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #185) #("URI" 0 3 (:parent #189))) #("to something like\n" 0 18 (:parent #185))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #176))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #167))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #170))) :mode section :granularity nil :parent #167) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #170) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #173) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #176))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #180) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #191) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #194))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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Follow the instructions on\n" 0 117 (:parent #158)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #158))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #153) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #156) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #159)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #159) #("default" 0 7 (:parent #163)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #163) #("settings.py" 0 11 (:parent #167)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #159))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #156) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #161))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #156) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #163))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #154))) :mode nil :granularity nil :parent #146) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #154) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #157) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #160)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #160) #("README" 0 6 (:parent #164))) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #155) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #158) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #161))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #156))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #159))) :mode section :granularity nil :parent #156) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #159) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #162) #("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 #165))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #162) #("As root configure the Guix profile\n" 0 35 (:parent #166))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #162) #("and run for example\n" 0 20 (:parent #168))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #162) #("If you want to run as root you may have to set\n" 0 47 (:parent #170))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #162) #("You also need to set\n" 0 21 (:parent #172))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #162) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #174))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #162) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #175))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #162) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #177))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #162) #("When you get errors like:\n" 0 26 (:parent #179))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #162) #("you may need to set\n" 0 20 (:parent #181))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #162)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #160))) :mode nil :granularity nil :parent #156) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #160) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #163) #("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 #166)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #170))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #166) #("s" 0 1 (:parent #171))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #166)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #166) #("plant" 0 5 (:parent #174))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #166))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #163) #("Download one database from\n" 0 27 (:parent #167))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #163) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\n" 0 1 (:parent #168))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #163) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #169))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #163) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #171))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #163)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #163) #("and\n" 0 4 (:parent #174))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #163) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #176))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #163) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #178))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #163) #("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 #179))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #163) #("Note for the plant database you can rename it to db" 0 51 (:parent #180)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #180) #("webqtl" 0 6 (:parent #184))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #180) #("s" 0 1 (:parent #185))) #(", or\nchange the settings in etc/default" 0 39 (:parent #180)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #180) #("settings.py" 0 11 (:parent #187))) #("to match your path.\n" 0 20 (:parent #180)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #157) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #160) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #163)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\n" 0 1 (:parent #163))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #158))) :mode nil :granularity nil :parent #146) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #158) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #161) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #164))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #161) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #("\n" 0 1 (:parent #165))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #159) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #162) #("See " 0 4 (:parent #165)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #(".\n" 0 2 (:parent #165))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #160))) :mode nil :granularity nil :parent #146) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #160) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #163) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #166)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #166))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #161))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #164))) :mode section :granularity nil :parent #161) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #164) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #167) #("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 #170)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #170) #("PATH" 0 4 (:parent #174))) #("and R" 0 5 (:parent #170)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #170) #("LIBS" 0 4 (:parent #176))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #170) #("SITE" 0 4 (:parent #177))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #170))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #167) #("On one system:\n" 0 15 (:parent #172))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #167) #("and perhaps a few more.\n" 0 24 (:parent #174))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #165)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #165) #("data" 0 4 (:parent #207))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #165)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #165) #("files" 0 5 (:parent #209))) #("/genotype'" 0 10 (:parent #165))) :mode nil :granularity nil :parent #161) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #165) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #168) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #171)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #171) #("data" 0 4 (:parent #175))) #(". 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 #171)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #171) #("settings.py" 0 11 (:parent #177))) #("(see above in\nthis document).\n" 0 30 (:parent #171))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #168) #("You can use the GENENETWORK" 0 27 (:parent #172)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #172) #("FILES" 0 5 (:parent #176))) #("switch to set the datadir, for example\n" 0 39 (:parent #172))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #168)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #166))) :mode nil :granularity nil :parent #161) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #166) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #169) #("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 #172))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #167))) :mode nil :granularity nil :parent #161) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #167) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #170) #("This error\n" 0 11 (:parent #173))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #170) #("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 #175))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #170) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #176)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #176) #("LIBS" 0 4 (:parent #180))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #176) #("SITE" 0 4 (:parent #181))) #(". 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 #176))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #168))) :mode nil :granularity nil :parent #161) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #168) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #171) #("The following error\n" 0 20 (:parent #174))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #171)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #171) #("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 #176))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #171)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #171) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #178))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #171)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #171) #("if that works run genenetwork after setting SQL" 0 47 (:parent #180)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #180) #("URI" 0 3 (:parent #184))) #("to something like\n" 0 18 (:parent #180))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #171))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #162))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #165))) :mode section :granularity nil :parent #162) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #165) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #168) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #171))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #168) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #175) #("Base install\n" 0 13 (:parent #178))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #175) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #182) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #185)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #183) #("Get Guix build going\n" 0 21 (:parent #186))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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:contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #343) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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"- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #367) #("Base install\n" 0 13 (:parent #370))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #374) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #377)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #375) #("Get Guix build going\n" 0 21 (:parent #378))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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"http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #386)) #("\n" 0 1 (:parent #386)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #379) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #384) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #387)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #376) #("Create a gn2 user and home with space\n" 0 38 (:parent #379)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #378) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #381))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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(:parent #157)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #157) #("complex" 0 7 (:parent #161))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #157)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #157) #("Guix-notes" 0 10 (:parent #163))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #157))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #154) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #158) #("Guix bioinformatics" 0 19 (:parent #162))) #("and " 0 4 (:parent #158)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #158) #("GNU Guix" 0 8 (:parent #164))) #(".\n" 0 2 (:parent #158))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #154) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #159)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #159) #("GN2 Dependency Graph" 0 20 (:parent #163))) #(".\n" 0 2 (:parent #159))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #152) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #155) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #158)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #158)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #158))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #153) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #156) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #159)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #159) #("default" 0 7 (:parent #163)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #163) #("settings.py" 0 11 (:parent #167)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #159))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #156) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #161))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #156)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #156) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #163))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #154))) :mode nil :granularity nil :parent #146) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #154) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #157) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #160)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #160) #("README" 0 6 (:parent #164))) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #155))) :mode nil :granularity nil :parent #146) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #155) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #158) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #161))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #156))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #159))) :mode section :granularity nil :parent #156) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #159) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #162) #("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 #165))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #162) #("As root configure the Guix profile\n" 0 35 (:parent #166))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #162) #("and run for example\n" 0 20 (:parent #168))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #162)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #162) #("If you want to run as root you may have to set\n" 0 47 (:parent #170))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #162) #("You also need to set\n" 0 21 (:parent #172))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #162) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #174))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #162) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #175))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #162) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #177))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #162) #("When you get errors like:\n" 0 26 (:parent #179))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #162)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #162) #("you may need to set\n" 0 20 (:parent #181))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #162)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #160))) :mode nil :granularity nil :parent #156) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #160) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #163) #("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 #166)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #170))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #166) #("s" 0 1 (:parent #171))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #166)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #166) #("plant" 0 5 (:parent #174))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #166))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #163) #("Download one database from\n" 0 27 (:parent #167))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #163) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #("\n" 0 1 (:parent #168))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #163) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #169))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #163) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #171))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #163)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #163) #("and\n" 0 4 (:parent #174))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #163) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #176))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #163)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #163) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #178))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #163) #("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 #179))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #163) #("Note for the plant database you can rename it to db" 0 51 (:parent #180)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #180) #("webqtl" 0 6 (:parent #184))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #180) #("s" 0 1 (:parent #185))) #(", or\nchange the settings in etc/default" 0 39 (:parent #180)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #180) #("settings.py" 0 11 (:parent #187))) #("to match your path.\n" 0 20 (:parent #180)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #157))) :mode nil :granularity nil :parent #146) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #157) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #160) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #163)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #163)) #("\n" 0 1 (:parent #163))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #158))) :mode nil :granularity nil :parent #146) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #158) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #161) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #164))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #161) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #("\n" 0 1 (:parent #165))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #159))) :mode nil :granularity nil :parent #146) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #159) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #162) #("See " 0 4 (:parent #165)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #165)) #(".\n" 0 2 (:parent #165))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #160))) :mode nil :granularity nil :parent #146) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #160) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #163) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #166)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #166))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #161))) :mode nil :granularity nil :parent #146) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #164))) :mode section :granularity nil :parent #161) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #164) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #167) #("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 #170)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #170) #("PATH" 0 4 (:parent #174))) #("and R" 0 5 (:parent #170)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #170) #("LIBS" 0 4 (:parent #176))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #170) #("SITE" 0 4 (:parent #177))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #170))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #167) #("On one system:\n" 0 15 (:parent #172))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #167)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #167) #("and perhaps a few more.\n" 0 24 (:parent #174))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #165)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #165) #("data" 0 4 (:parent #207))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #165)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #165) #("files" 0 5 (:parent #209))) #("/genotype'" 0 10 (:parent #165))) :mode nil :granularity nil :parent #161) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #165) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #168) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #171)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #171) #("data" 0 4 (:parent #175))) #(". 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 #171)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #171) #("settings.py" 0 11 (:parent #177))) #("(see above in\nthis document).\n" 0 30 (:parent #171))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #168) #("You can use the GENENETWORK" 0 27 (:parent #172)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #172) #("FILES" 0 5 (:parent #176))) #("switch to set the datadir, for example\n" 0 39 (:parent #172))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #168)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #166))) :mode nil :granularity nil :parent #161) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #166) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #169) #("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 #172))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #167))) :mode nil :granularity nil :parent #161) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #167) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #170) #("This error\n" 0 11 (:parent #173))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #170) #("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 #175))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #170) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #176)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #176) #("LIBS" 0 4 (:parent #180))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #176) #("SITE" 0 4 (:parent #181))) #(". 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 #176))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #168))) :mode nil :granularity nil :parent #161) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #168) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #171) #("The following error\n" 0 20 (:parent #174))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #171)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #171) #("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 #176))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #171)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #171) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #178))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #171)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #171) #("if that works run genenetwork after setting SQL" 0 47 (:parent #180)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #180) #("URI" 0 3 (:parent #184))) #("to something like\n" 0 18 (:parent #180))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #171))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #162))) :mode nil :granularity nil :parent #146) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #165))) :mode section :granularity nil :parent #162) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #165) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #168) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #171))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #168) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #175) #("Base install\n" 0 13 (:parent #178))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #175) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #182) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #185)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #183) #("Get Guix build going\n" 0 21 (:parent #186))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #183) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #187) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #190) #("Build the correct version of Guix\n" 0 34 (:parent #193)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #187) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #191) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #194)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #187) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #192) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #195)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #184) #("Create a gn2 user and home with space\n" 0 38 (:parent #187)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #179) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #185) #("Install redis\n" 0 14 (:parent #188))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #185) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 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40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #147) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #150))) #101 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #152) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #155) #("Large system deployments can get very " 0 38 (:parent #158)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #158) #("complex" 0 7 (:parent #162))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #158)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #158) #("Guix-notes" 0 10 (:parent #164))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #158))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #155) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #159) #("Guix bioinformatics" 0 19 (:parent #163))) #("and " 0 4 (:parent #159)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #159) #("GNU Guix" 0 8 (:parent #165))) #(".\n" 0 2 (:parent #159))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #155) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #160)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #160) #("GN2 Dependency Graph" 0 20 (:parent #164))) #(".\n" 0 2 (:parent #160))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #153) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #156) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #159)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #159)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #159))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #154) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #157) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #160)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #160) #("default" 0 7 (:parent #164)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #164) #("settings.py" 0 11 (:parent #168)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #160))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #157)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #157) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #162))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #157)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #157) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #164))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #155))) :mode nil :granularity nil :parent #147) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #155) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #158) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #161)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #161) #("README" 0 6 (:parent #165))) #(".\n" 0 2 (:parent #161))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #156))) :mode nil :granularity nil :parent #147) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #156) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #159) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #162))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #157))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #160))) :mode section :granularity nil :parent #157) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #160) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #163) #("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 #166))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #163) #("As root configure the Guix profile\n" 0 35 (:parent #167))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #163)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #163) #("and run for example\n" 0 20 (:parent #169))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #163)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #163) #("If you want to run as root you may have to set\n" 0 47 (:parent #171))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #163)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #163) #("You also need to set\n" 0 21 (:parent #173))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #163)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #163) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #175))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #163) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #176))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #163)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #163) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #178))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #163)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #163) #("When you get errors like:\n" 0 26 (:parent #180))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #163)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #163) #("you may need to set\n" 0 20 (:parent #182))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #163)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #161))) :mode nil :granularity nil :parent #157) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #161) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #164) #("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 #167)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #167) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #167) #("s" 0 1 (:parent #172))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #167)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #167) #("webqtl" 0 6 (:parent #174))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #167) #("plant" 0 5 (:parent #175))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #167))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #164) #("Download one database from\n" 0 27 (:parent #168))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #164) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #("\n" 0 1 (:parent #169))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #164) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #170))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #164)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #164) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #172))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #164)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #164)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #164) #("and\n" 0 4 (:parent #175))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #164)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #164) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #177))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #164)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #164) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #179))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #164) #("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 #180))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #164) #("Note for the plant database you can rename it to db" 0 51 (:parent #181)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #181) #("webqtl" 0 6 (:parent #185))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #181) #("s" 0 1 (:parent #186))) #(", or\nchange the settings in etc/default" 0 39 (:parent #181)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #181) #("settings.py" 0 11 (:parent #188))) #("to match your path.\n" 0 20 (:parent #181)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #158))) :mode nil :granularity nil :parent #147) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #158) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #161) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #164)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #164)) #("\n" 0 1 (:parent #164))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #161)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #159))) :mode nil :granularity nil :parent #147) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #159) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #162) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #165))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #162) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #("\n" 0 1 (:parent #166))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #160))) :mode nil :granularity nil :parent #147) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #160) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #163) #("See " 0 4 (:parent #166)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #166)) #(".\n" 0 2 (:parent #166))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #161))) :mode nil :granularity nil :parent #147) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #161) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #164) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #167)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #167))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #162))) :mode nil :granularity nil :parent #147) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #165))) :mode section :granularity nil :parent #162) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #165) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #168) #("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 #171)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #171) #("PATH" 0 4 (:parent #175))) #("and R" 0 5 (:parent #171)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #171) #("LIBS" 0 4 (:parent #177))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #171) #("SITE" 0 4 (:parent #178))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #171))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #168)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #168) #("On one system:\n" 0 15 (:parent #173))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #168)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #168) #("and perhaps a few more.\n" 0 24 (:parent #175))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #166)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #166) #("data" 0 4 (:parent #208))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #166)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #166) #("files" 0 5 (:parent #210))) #("/genotype'" 0 10 (:parent #166))) :mode nil :granularity nil :parent #162) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #166) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #169) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #172)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #172) #("data" 0 4 (:parent #176))) #(". 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 #172)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #172) #("settings.py" 0 11 (:parent #178))) #("(see above in\nthis document).\n" 0 30 (:parent #172))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #169) #("You can use the GENENETWORK" 0 27 (:parent #173)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #173) #("FILES" 0 5 (:parent #177))) #("switch to set the datadir, for example\n" 0 39 (:parent #173))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #169)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #167))) :mode nil :granularity nil :parent #162) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #167) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #170) #("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 #173))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #168))) :mode nil :granularity nil :parent #162) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #168) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #171) #("This error\n" 0 11 (:parent #174))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #171)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #171) #("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 #176))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #171) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #177)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #177) #("LIBS" 0 4 (:parent #181))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #177) #("SITE" 0 4 (:parent #182))) #(". 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 #177))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #169))) :mode nil :granularity nil :parent #162) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #169) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #172) #("The following error\n" 0 20 (:parent #175))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #172)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #172) #("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 #177))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #172)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #172) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #179))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #172)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #172) #("if that works run genenetwork after setting SQL" 0 47 (:parent #181)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #181) #("URI" 0 3 (:parent #185))) #("to something like\n" 0 18 (:parent #181))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #172))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #163))) :mode nil :granularity nil :parent #147) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #166))) :mode section :granularity nil :parent #163) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #166) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #169) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #172))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #176) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #187) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #190))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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Follow the instructions on\n" 0 117 (:parent #138)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #138)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #138))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #133) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #136) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #139)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #139) #("default" 0 7 (:parent #143)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #143) #("settings.py" 0 11 (:parent #147)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #139))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #136) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #141))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #136) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #143))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #134))) :mode nil :granularity nil :parent #126) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #134) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #137) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #140)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #140) #("README" 0 6 (:parent #144))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #135) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #138) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #141))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #136))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #139))) :mode section :granularity nil :parent #136) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #139) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #142) #("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 #145))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #142) #("As root configure the Guix profile\n" 0 35 (:parent #146))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #142) #("and run for example\n" 0 20 (:parent #148))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #142) #("If you want to run as root you may have to set\n" 0 47 (:parent #150))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #142) #("You also need to set\n" 0 21 (:parent #152))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #142) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #154))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #142) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #155))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #142) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #157))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #142) #("When you get errors like:\n" 0 26 (:parent #159))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #142) #("you may need to set\n" 0 20 (:parent #161))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #140))) :mode nil :granularity nil :parent #136) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #140) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #143) #("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 #146)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #150))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #146) #("s" 0 1 (:parent #151))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #146)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #146) #("plant" 0 5 (:parent #154))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #146))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #143) #("Download one database from\n" 0 27 (:parent #147))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #143) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #143) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #149))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #143) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #151))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #143)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #143) #("and\n" 0 4 (:parent #154))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #143) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #156))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #143) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #158))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #143) #("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 #159))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #143) #("Note for the plant database you can rename it to db" 0 51 (:parent #160)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #160) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #160) #("s" 0 1 (:parent #165))) #(", or\nchange the settings in etc/default" 0 39 (:parent #160)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #160) #("settings.py" 0 11 (:parent #167))) #("to match your path.\n" 0 20 (:parent #160)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #137) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #140) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #143)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #("\n" 0 1 (:parent #143))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #138))) :mode nil :granularity nil :parent #126) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #138) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #141) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #144))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #141) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #139) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #142) #("See " 0 4 (:parent #145)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #140))) :mode nil :granularity nil :parent #126) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #140) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #143) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #146)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #146))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #141))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #144) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #147) #("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 #150)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #150) #("PATH" 0 4 (:parent #154))) #("and R" 0 5 (:parent #150)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #150) #("LIBS" 0 4 (:parent #156))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #150) #("SITE" 0 4 (:parent #157))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #150))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #147) #("On one system:\n" 0 15 (:parent #152))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #147) #("and perhaps a few more.\n" 0 24 (:parent #154))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #145)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #145) #("data" 0 4 (:parent #187))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #145)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #145) #("files" 0 5 (:parent #189))) #("/genotype'" 0 10 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #145) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #148) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #151)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #151) #("data" 0 4 (:parent #155))) #(". 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 #151)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #151) #("settings.py" 0 11 (:parent #157))) #("(see above in\nthis document).\n" 0 30 (:parent #151))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #148) #("You can use the GENENETWORK" 0 27 (:parent #152)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #152) #("FILES" 0 5 (:parent #156))) #("switch to set the datadir, for example\n" 0 39 (:parent #152))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #146))) :mode nil :granularity nil :parent #141) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #146) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #149) #("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 #152))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #147))) :mode nil :granularity nil :parent #141) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #147) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #150) #("This error\n" 0 11 (:parent #153))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #150) #("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 #155))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #150) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #156)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #156) #("SITE" 0 4 (:parent #161))) #(". 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 #156))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #148))) :mode nil :granularity nil :parent #141) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #148) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #151) #("The following error\n" 0 20 (:parent #154))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #151) #("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 #156))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #151)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #151) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #158))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #151)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #151) #("if that works run genenetwork after setting SQL" 0 47 (:parent #160)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #160) #("URI" 0 3 (:parent #164))) #("to something like\n" 0 18 (:parent #160))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #151))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #142))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #145) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #148) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #151))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #148) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #152) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #155) #("Base install\n" 0 13 (:parent #158))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #155) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #162) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #165)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #163) #("Get Guix build going\n" 0 21 (:parent #166))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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:contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #343) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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"- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #367) #("Base install\n" 0 13 (:parent #370))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #374) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #377)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #375) #("Get Guix build going\n" 0 21 (:parent #378))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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"http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #386)) #("\n" 0 1 (:parent #386)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #379) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #384) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #387)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #376) #("Create a gn2 user and home with space\n" 0 38 (:parent #379)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #378) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #381))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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:post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #129))) #80 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #131))) :mode nil :granularity nil :parent #126) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #131) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #134) #("Large system deployments can get very " 0 38 (:parent #137)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #137)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #137) #("Guix-notes" 0 10 (:parent #143))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #137))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #134) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #138) #("Guix bioinformatics" 0 19 (:parent #142))) #("and " 0 4 (:parent #138)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #138) #("GNU Guix" 0 8 (:parent #144))) #(".\n" 0 2 (:parent #138))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #134) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #139)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #139) #("GN2 Dependency Graph" 0 20 (:parent #143))) #(".\n" 0 2 (:parent #139))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #132))) :mode nil :granularity nil :parent #126) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #132) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #135) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #138)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #138)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #138))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #133))) :mode nil :granularity nil :parent #126) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #133) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #136) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #139)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #139) #("default" 0 7 (:parent #143)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #143) #("settings.py" 0 11 (:parent #147)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #139))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #136) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #141))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #136)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #136) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #143))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #134))) :mode nil :granularity nil :parent #126) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #134) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #137) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #140)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #140) #("README" 0 6 (:parent #144))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #135))) :mode nil :granularity nil :parent #126) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #135) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #138) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #141))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #136))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #139))) :mode section :granularity nil :parent #136) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #139) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #142) #("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 #145))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #142) #("As root configure the Guix profile\n" 0 35 (:parent #146))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #142) #("and run for example\n" 0 20 (:parent #148))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #142)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #142) #("If you want to run as root you may have to set\n" 0 47 (:parent #150))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #142) #("You also need to set\n" 0 21 (:parent #152))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #142) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #154))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #142) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #155))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #142) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #157))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #142) #("When you get errors like:\n" 0 26 (:parent #159))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #142)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #142) #("you may need to set\n" 0 20 (:parent #161))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #140))) :mode nil :granularity nil :parent #136) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #140) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #143) #("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 #146)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #150))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #146) #("s" 0 1 (:parent #151))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #146)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #146) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #146) #("plant" 0 5 (:parent #154))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #146))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #143) #("Download one database from\n" 0 27 (:parent #147))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #143) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #143) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #149))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #143) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #151))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #143)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #143) #("and\n" 0 4 (:parent #154))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #143) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #156))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #143)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #143) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #158))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #143) #("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 #159))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #143) #("Note for the plant database you can rename it to db" 0 51 (:parent #160)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #160) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #160) #("s" 0 1 (:parent #165))) #(", or\nchange the settings in etc/default" 0 39 (:parent #160)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #160) #("settings.py" 0 11 (:parent #167))) #("to match your path.\n" 0 20 (:parent #160)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #137))) :mode nil :granularity nil :parent #126) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #137) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #140) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #143)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #143)) #("\n" 0 1 (:parent #143))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #140)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #138))) :mode nil :granularity nil :parent #126) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #138) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #141) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #144))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #141) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #139))) :mode nil :granularity nil :parent #126) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #139) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #142) #("See " 0 4 (:parent #145)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #140))) :mode nil :granularity nil :parent #126) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #140) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #143) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #146)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #146))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #141))) :mode nil :granularity nil :parent #126) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #144) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #147) #("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 #150)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #150) #("PATH" 0 4 (:parent #154))) #("and R" 0 5 (:parent #150)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #150) #("LIBS" 0 4 (:parent #156))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #150) #("SITE" 0 4 (:parent #157))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #150))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #147) #("On one system:\n" 0 15 (:parent #152))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #147)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #147) #("and perhaps a few more.\n" 0 24 (:parent #154))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #145)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #145) #("data" 0 4 (:parent #187))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #145)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #145) #("files" 0 5 (:parent #189))) #("/genotype'" 0 10 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #145) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #148) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #151)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #151) #("data" 0 4 (:parent #155))) #(". 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 #151)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #151) #("settings.py" 0 11 (:parent #157))) #("(see above in\nthis document).\n" 0 30 (:parent #151))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #148) #("You can use the GENENETWORK" 0 27 (:parent #152)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #152) #("FILES" 0 5 (:parent #156))) #("switch to set the datadir, for example\n" 0 39 (:parent #152))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #146))) :mode nil :granularity nil :parent #141) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #146) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #149) #("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 #152))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #147))) :mode nil :granularity nil :parent #141) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #147) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #150) #("This error\n" 0 11 (:parent #153))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #150)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #150) #("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 #155))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #150) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #156)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #156) #("SITE" 0 4 (:parent #161))) #(". 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 #156))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #148))) :mode nil :granularity nil :parent #141) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #148) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #151) #("The following error\n" 0 20 (:parent #154))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #151) #("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 #156))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #151)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #151) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #158))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #151)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #151) #("if that works run genenetwork after setting SQL" 0 47 (:parent #160)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #160) #("URI" 0 3 (:parent #164))) #("to something like\n" 0 18 (:parent #160))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #151))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #142))) :mode nil :granularity nil :parent #126) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #145) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #148) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #151))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #148) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #152) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #155) #("Base install\n" 0 13 (:parent #158))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #155) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #162) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #165)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #163) #("Get Guix build going\n" 0 21 (:parent #166))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #163) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #167) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #170) #("Build the correct version of Guix\n" 0 34 (:parent #173)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #167) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #171) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #174)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #174)) #("\n" 0 1 (:parent #174)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #167) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #172) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #175)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #164) #("Create a gn2 user and home with space\n" 0 38 (:parent #167)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #165) #("Install redis\n" 0 14 (:parent #168))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #165) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 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40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #127) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #130))) #81 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #132))) :mode nil :granularity nil :parent #127) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #132) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #135) #("Large system deployments can get very " 0 38 (:parent #138)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #138) #("complex" 0 7 (:parent #142))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #138)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #138) #("Guix-notes" 0 10 (:parent #144))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #138))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #135) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #139) #("Guix bioinformatics" 0 19 (:parent #143))) #("and " 0 4 (:parent #139)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #139) #("GNU Guix" 0 8 (:parent #145))) #(".\n" 0 2 (:parent #139))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #135) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #140)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #140) #("GN2 Dependency Graph" 0 20 (:parent #144))) #(".\n" 0 2 (:parent #140))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #133))) :mode nil :granularity nil :parent #127) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #133) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #136) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #139)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #139)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #139))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #134))) :mode nil :granularity nil :parent #127) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #134) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #137) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #140)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #140) #("default" 0 7 (:parent #144)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #144) #("settings.py" 0 11 (:parent #148)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #140))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #137) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #142))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #137)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #137) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #144))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #135))) :mode nil :granularity nil :parent #127) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #135) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #138) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #141)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #141) #("README" 0 6 (:parent #145))) #(".\n" 0 2 (:parent #141))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #136))) :mode nil :granularity nil :parent #127) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #136) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #139) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #142))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #137))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #140))) :mode section :granularity nil :parent #137) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #140) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #143) #("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 #146))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #143) #("As root configure the Guix profile\n" 0 35 (:parent #147))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #143) #("and run for example\n" 0 20 (:parent #149))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #143)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #143) #("If you want to run as root you may have to set\n" 0 47 (:parent #151))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #143) #("You also need to set\n" 0 21 (:parent #153))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #143) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #155))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #143) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #156))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #143) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #158))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #143) #("When you get errors like:\n" 0 26 (:parent #160))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #143)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #143) #("you may need to set\n" 0 20 (:parent #162))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #143)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #141))) :mode nil :granularity nil :parent #137) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #141) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #144) #("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 #147)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #147) #("webqtl" 0 6 (:parent #151))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #147) #("s" 0 1 (:parent #152))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #147)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #147) #("webqtl" 0 6 (:parent #154))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #147) #("plant" 0 5 (:parent #155))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #147))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #144) #("Download one database from\n" 0 27 (:parent #148))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #144) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #144) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #150))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #144) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #152))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #144)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #144) #("and\n" 0 4 (:parent #155))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #144) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #157))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #144)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #144) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #159))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #144) #("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 #160))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #144) #("Note for the plant database you can rename it to db" 0 51 (:parent #161)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #161) #("webqtl" 0 6 (:parent #165))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #161) #("s" 0 1 (:parent #166))) #(", or\nchange the settings in etc/default" 0 39 (:parent #161)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #161) #("settings.py" 0 11 (:parent #168))) #("to match your path.\n" 0 20 (:parent #161)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #138))) :mode nil :granularity nil :parent #127) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #138) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #141) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #144)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #144)) #("\n" 0 1 (:parent #144))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #141)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #139))) :mode nil :granularity nil :parent #127) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #139) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #142) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #145))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #142) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #140))) :mode nil :granularity nil :parent #127) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #140) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #143) #("See " 0 4 (:parent #146)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #141))) :mode nil :granularity nil :parent #127) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #141) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #144) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #147)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #147))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #142))) :mode nil :granularity nil :parent #127) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #145) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #148) #("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 #151)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #151) #("PATH" 0 4 (:parent #155))) #("and R" 0 5 (:parent #151)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #151) #("LIBS" 0 4 (:parent #157))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #151) #("SITE" 0 4 (:parent #158))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #151))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #148) #("On one system:\n" 0 15 (:parent #153))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #148)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #148) #("and perhaps a few more.\n" 0 24 (:parent #155))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #146)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #146) #("data" 0 4 (:parent #188))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #146)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #146) #("files" 0 5 (:parent #190))) #("/genotype'" 0 10 (:parent #146))) :mode nil :granularity nil :parent #142) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #146) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #149) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #152)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #152) #("data" 0 4 (:parent #156))) #(". 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 #152)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #152) #("settings.py" 0 11 (:parent #158))) #("(see above in\nthis document).\n" 0 30 (:parent #152))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #149) #("You can use the GENENETWORK" 0 27 (:parent #153)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #153) #("FILES" 0 5 (:parent #157))) #("switch to set the datadir, for example\n" 0 39 (:parent #153))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #147))) :mode nil :granularity nil :parent #142) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #147) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #150) #("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 #153))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #148))) :mode nil :granularity nil :parent #142) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #148) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #151) #("This error\n" 0 11 (:parent #154))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #151)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #151) #("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 #156))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #151) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #157)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #157) #("LIBS" 0 4 (:parent #161))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #157) #("SITE" 0 4 (:parent #162))) #(". 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 #157))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #149))) :mode nil :granularity nil :parent #142) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #149) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #152) #("The following error\n" 0 20 (:parent #155))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #152) #("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 #157))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #152)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #152) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #159))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #152)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #152) #("if that works run genenetwork after setting SQL" 0 47 (:parent #161)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #161) #("URI" 0 3 (:parent #165))) #("to something like\n" 0 18 (:parent #161))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #152))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #143))) :mode nil :granularity nil :parent #127) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #146) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #149) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #152))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #156) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #167) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #170))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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:contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #136) #("Large system deployments can get very " 0 38 (:parent #139)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #139) #("complex" 0 7 (:parent #143))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #139)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #139) #("Guix-notes" 0 10 (:parent #145))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #139))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #136) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #140) #("Guix bioinformatics" 0 19 (:parent #144))) #("and " 0 4 (:parent #140)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #140) #("GNU Guix" 0 8 (:parent #146))) #(".\n" 0 2 (:parent #140))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #136) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #141)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #141) #("GN2 Dependency Graph" 0 20 (:parent #145))) #(".\n" 0 2 (:parent #141))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #134))) :mode nil :granularity nil :parent #128) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #134) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #137) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #140)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #140)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #140))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #135))) :mode nil :granularity nil :parent #128) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #135) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #138) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #141)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #141) #("default" 0 7 (:parent #145)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #145) #("settings.py" 0 11 (:parent #149)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #141))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #138) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #143))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #138)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #138) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #145))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #136))) :mode nil :granularity nil :parent #128) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #136) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #139) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #142)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #142) #("README" 0 6 (:parent #146))) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #137))) :mode nil :granularity nil :parent #128) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #137) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #140) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #143))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #138))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #141))) :mode section :granularity nil :parent #138) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #141) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #144) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #147))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #144) #("As root configure the Guix profile\n" 0 35 (:parent #148))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #144) #("and run for example\n" 0 20 (:parent #150))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #144)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #144) #("If you want to run as root you may have to set\n" 0 47 (:parent #152))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #144) #("You also need to set\n" 0 21 (:parent #154))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #144) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #156))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #144) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #157))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #144) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #159))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #144) #("When you get errors like:\n" 0 26 (:parent #161))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #144)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #144) #("you may need to set\n" 0 20 (:parent #163))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #142))) :mode nil :granularity nil :parent #138) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #142) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #145) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #148)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #152))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #148) #("s" 0 1 (:parent #153))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #148)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #148) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #148) #("plant" 0 5 (:parent #156))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #148))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #145) #("Download one database from\n" 0 27 (:parent #149))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #145) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #145) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #151))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #145) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #153))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #145)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #145) #("and\n" 0 4 (:parent #156))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #145) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #158))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #145)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #145) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #160))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #145) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #161))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #145) #("Note for the plant database you can rename it to db" 0 51 (:parent #162)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #162) #("webqtl" 0 6 (:parent #166))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #162) #("s" 0 1 (:parent #167))) #(", or\nchange the settings in etc/default" 0 39 (:parent #162)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #169))) #("to match your path.\n" 0 20 (:parent #162)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #139))) :mode nil :granularity nil :parent #128) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #139) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #142) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #145)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #145)) #("\n" 0 1 (:parent #145))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #142)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #140))) :mode nil :granularity nil :parent #128) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #140) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #143) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #146))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #143) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #141))) :mode nil :granularity nil :parent #128) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #141) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #144) #("See " 0 4 (:parent #147)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #142))) :mode nil :granularity nil :parent #128) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #142) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #145) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #148)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #148))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #143))) :mode nil :granularity nil :parent #128) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #146) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #149) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #152)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #152) #("PATH" 0 4 (:parent #156))) #("and R" 0 5 (:parent #152)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #152) #("LIBS" 0 4 (:parent #158))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #152) #("SITE" 0 4 (:parent #159))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #152))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #149) #("On one system:\n" 0 15 (:parent #154))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #149)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #149) #("and perhaps a few more.\n" 0 24 (:parent #156))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #147)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #147) #("data" 0 4 (:parent #189))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #147)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #147) #("files" 0 5 (:parent #191))) #("/genotype'" 0 10 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #147) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #150) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #153)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #153) #("data" 0 4 (:parent #157))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #153)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #153) #("settings.py" 0 11 (:parent #159))) #("(see above in\nthis document).\n" 0 30 (:parent #153))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #150) #("You can use the GENENETWORK" 0 27 (:parent #154)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #154) #("FILES" 0 5 (:parent #158))) #("switch to set the datadir, for example\n" 0 39 (:parent #154))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #148))) :mode nil :granularity nil :parent #143) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #148) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #151) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #154))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #149))) :mode nil :granularity nil :parent #143) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #149) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #152) #("This error\n" 0 11 (:parent #155))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #152)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #152) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #157))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #152) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #158)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #158) #("SITE" 0 4 (:parent #163))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #158))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #150))) :mode nil :granularity nil :parent #143) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #150) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #153) #("The following error\n" 0 20 (:parent #156))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #153) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #158))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #153)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #153) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #160))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #153)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #153) #("if that works run genenetwork after setting SQL" 0 47 (:parent #162)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #162) #("URI" 0 3 (:parent #166))) #("to something like\n" 0 18 (:parent #162))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #153))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #144))) :mode nil :granularity nil :parent #128) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #147) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #150) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #153))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #150) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #154) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #157) #("Base install\n" 0 13 (:parent #160))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #157) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #164) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #167)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #165) #("Get Guix build going\n" 0 21 (:parent #168))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #165) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #172) #("Build the correct version of Guix\n" 0 34 (:parent #175)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #173) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #176)) (link (:type "http" :path "//git.genenetwork.org/pjotrp/guix-bioinformatics" :format plain :raw-link "http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #176)) #("\n" 0 1 (:parent #176)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #174) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #177)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #166) #("Create a gn2 user and home with space\n" 0 38 (:parent #169)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #161) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #167) #("Install redis\n" 0 14 (:parent #170))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #167) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #174) #("add to systemd\n" 0 15 (:parent #177)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 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 #140)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #140) #("Guix-notes" 0 10 (:parent #146))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #140))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #137) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #141) #("Guix bioinformatics" 0 19 (:parent #145))) #("and " 0 4 (:parent #141)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #141) #("GNU Guix" 0 8 (:parent #147))) #(".\n" 0 2 (:parent #141))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #137) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #142)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #142) #("GN2 Dependency Graph" 0 20 (:parent #146))) #(".\n" 0 2 (:parent #142))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #135))) :mode nil :granularity nil :parent #129) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #135) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #138) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #141)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #141)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #141))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #136))) :mode nil :granularity nil :parent #129) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #136) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #139) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #142)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #142) #("default" 0 7 (:parent #146)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #146) #("settings.py" 0 11 (:parent #150)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #142))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #139)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #139) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #144))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #139)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #139) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #146))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #137))) :mode nil :granularity nil :parent #129) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #137) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #140) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #143)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #143) #("README" 0 6 (:parent #147))) #(".\n" 0 2 (:parent #143))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #138))) :mode nil :granularity nil :parent #129) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #138) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #141) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #144))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #139))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #142))) :mode section :granularity nil :parent #139) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #142) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #145) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #148))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #145) #("As root configure the Guix profile\n" 0 35 (:parent #149))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #145) #("and run for example\n" 0 20 (:parent #151))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #145)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #145) #("If you want to run as root you may have to set\n" 0 47 (:parent #153))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #145) #("You also need to set\n" 0 21 (:parent #155))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #145) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #157))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #145) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #158))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #145) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #160))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #145) #("When you get errors like:\n" 0 26 (:parent #162))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #145)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #145) #("you may need to set\n" 0 20 (:parent #164))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #143))) :mode nil :granularity nil :parent #139) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #143) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #146) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #149)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #153))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #149) #("s" 0 1 (:parent #154))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #149)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #149) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #149) #("plant" 0 5 (:parent #157))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #149))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #146) #("Download one database from\n" 0 27 (:parent #150))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #146) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #146) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #152))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #146) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #154))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #146)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #146) #("and\n" 0 4 (:parent #157))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #146) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #159))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #146)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #146) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #161))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #146) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #162))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #146) #("Note for the plant database you can rename it to db" 0 51 (:parent #163)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #163) #("webqtl" 0 6 (:parent #167))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #163) #("s" 0 1 (:parent #168))) #(", or\nchange the settings in etc/default" 0 39 (:parent #163)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #163) #("settings.py" 0 11 (:parent #170))) #("to match your path.\n" 0 20 (:parent #163)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #140))) :mode nil :granularity nil :parent #129) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #140) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #143) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #146)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #146)) #("\n" 0 1 (:parent #146))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #143)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #141))) :mode nil :granularity nil :parent #129) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #141) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #144) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #147))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #144) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #142))) :mode nil :granularity nil :parent #129) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #142) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #145) #("See " 0 4 (:parent #148)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #143))) :mode nil :granularity nil :parent #129) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #143) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #146) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #149)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #149))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #144))) :mode nil :granularity nil :parent #129) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #147) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #150) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #153)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #153) #("PATH" 0 4 (:parent #157))) #("and R" 0 5 (:parent #153)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #153) #("LIBS" 0 4 (:parent #159))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #153) #("SITE" 0 4 (:parent #160))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #153))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #150) #("On one system:\n" 0 15 (:parent #155))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #150)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #150) #("and perhaps a few more.\n" 0 24 (:parent #157))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #148)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #148) #("data" 0 4 (:parent #190))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #148)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #148) #("files" 0 5 (:parent #192))) #("/genotype'" 0 10 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #148) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #151) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #154)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #154) #("data" 0 4 (:parent #158))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #154)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #154) #("settings.py" 0 11 (:parent #160))) #("(see above in\nthis document).\n" 0 30 (:parent #154))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #151) #("You can use the GENENETWORK" 0 27 (:parent #155)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #155) #("FILES" 0 5 (:parent #159))) #("switch to set the datadir, for example\n" 0 39 (:parent #155))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #149))) :mode nil :granularity nil :parent #144) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #149) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #152) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #155))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #150))) :mode nil :granularity nil :parent #144) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #150) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #153) #("This error\n" 0 11 (:parent #156))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #153)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #153) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #158))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #153) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #159)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #159) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #159) #("SITE" 0 4 (:parent #164))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #159))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #151))) :mode nil :granularity nil :parent #144) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #151) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #154) #("The following error\n" 0 20 (:parent #157))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #154) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #159))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #154)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #154) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #161))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #154)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #154) #("if that works run genenetwork after setting SQL" 0 47 (:parent #163)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #163) #("URI" 0 3 (:parent #167))) #("to something like\n" 0 18 (:parent #163))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #154))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #145))) :mode nil :granularity nil :parent #129) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #148) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #151) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #154))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #151) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #155) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #158) #("Base install\n" 0 13 (:parent #161))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #158) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #162) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #165) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #168)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #162) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #166) #("Get Guix build going\n" 0 21 (:parent #169))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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:CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #130) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #133))) #84 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #135))) :mode nil :granularity nil :parent #130) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #135) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #138) #("Large system deployments can get very " 0 38 (:parent #141)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #141) #("complex" 0 7 (:parent #145))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #141)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #141) #("Guix-notes" 0 10 (:parent #147))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #141))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #138) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #142) #("Guix bioinformatics" 0 19 (:parent #146))) #("and " 0 4 (:parent #142)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #142) #("GNU Guix" 0 8 (:parent #148))) #(".\n" 0 2 (:parent #142))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #138) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #143)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #143) #("GN2 Dependency Graph" 0 20 (:parent #147))) #(".\n" 0 2 (:parent #143))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #136))) :mode nil :granularity nil :parent #130) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #136) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #139) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #142)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #142)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #142))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #137))) :mode nil :granularity nil :parent #130) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #137) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #140) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #143)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #143) #("default" 0 7 (:parent #147)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #147) #("settings.py" 0 11 (:parent #151)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #143))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #140)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #140) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #145))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #140)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #140) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #147))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #138))) :mode nil :granularity nil :parent #130) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #138) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #141) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #144)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #144) #("README" 0 6 (:parent #148))) #(".\n" 0 2 (:parent #144))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #139))) :mode nil :granularity nil :parent #130) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #139) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #142) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #145))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #140))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #143))) :mode section :granularity nil :parent #140) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #143) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #146) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #149))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #146) #("As root configure the Guix profile\n" 0 35 (:parent #150))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #146) #("and run for example\n" 0 20 (:parent #152))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #146)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #146) #("If you want to run as root you may have to set\n" 0 47 (:parent #154))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #146) #("You also need to set\n" 0 21 (:parent #156))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #146) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #158))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #146) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #159))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #146) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #161))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #146) #("When you get errors like:\n" 0 26 (:parent #163))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #146)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #146) #("you may need to set\n" 0 20 (:parent #165))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #144))) :mode nil :granularity nil :parent #140) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #144) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #147) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #150)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #154))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #150) #("s" 0 1 (:parent #155))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #150)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #150) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #150) #("plant" 0 5 (:parent #158))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #150))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #147) #("Download one database from\n" 0 27 (:parent #151))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #147) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #147) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #153))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #147) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #155))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #147)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #147) #("and\n" 0 4 (:parent #158))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #147) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #160))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #147)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #147) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #162))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #147) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #163))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #147) #("Note for the plant database you can rename it to db" 0 51 (:parent #164)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #164) #("webqtl" 0 6 (:parent #168))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #164) #("s" 0 1 (:parent #169))) #(", or\nchange the settings in etc/default" 0 39 (:parent #164)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #164) #("settings.py" 0 11 (:parent #171))) #("to match your path.\n" 0 20 (:parent #164)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #141))) :mode nil :granularity nil :parent #130) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #141) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #144) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #147)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #147)) #("\n" 0 1 (:parent #147))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #144)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #142))) :mode nil :granularity nil :parent #130) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #142) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #145) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #148))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #145) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #143))) :mode nil :granularity nil :parent #130) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #143) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #146) #("See " 0 4 (:parent #149)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #144))) :mode nil :granularity nil :parent #130) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #144) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #147) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #150)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #150))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #145))) :mode nil :granularity nil :parent #130) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #148) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #151) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #154)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #154) #("PATH" 0 4 (:parent #158))) #("and R" 0 5 (:parent #154)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #154) #("LIBS" 0 4 (:parent #160))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #154) #("SITE" 0 4 (:parent #161))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #154))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #151) #("On one system:\n" 0 15 (:parent #156))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #151)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #151) #("and perhaps a few more.\n" 0 24 (:parent #158))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #149)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #149) #("data" 0 4 (:parent #191))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #149)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #149) #("files" 0 5 (:parent #193))) #("/genotype'" 0 10 (:parent #149))) :mode nil :granularity nil :parent #145) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #149) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #152) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #155)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #155) #("data" 0 4 (:parent #159))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #155)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #155) #("settings.py" 0 11 (:parent #161))) #("(see above in\nthis document).\n" 0 30 (:parent #155))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #152) #("You can use the GENENETWORK" 0 27 (:parent #156)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #156) #("FILES" 0 5 (:parent #160))) #("switch to set the datadir, for example\n" 0 39 (:parent #156))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #150))) :mode nil :granularity nil :parent #145) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #150) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #153) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #156))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #151))) :mode nil :granularity nil :parent #145) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #151) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #154) #("This error\n" 0 11 (:parent #157))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #154)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #154) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #159))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #154) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #160)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #160) #("LIBS" 0 4 (:parent #164))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #160) #("SITE" 0 4 (:parent #165))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #160))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #152))) :mode nil :granularity nil :parent #145) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #152) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #155) #("The following error\n" 0 20 (:parent #158))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #155) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #160))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #155)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #155) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #162))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #155)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #155) #("if that works run genenetwork after setting SQL" 0 47 (:parent #164)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #164) #("URI" 0 3 (:parent #168))) #("to something like\n" 0 18 (:parent #164))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #155))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #146))) :mode nil :granularity nil :parent #130) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #149) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #152) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #155))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #159) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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nil :parent #172) #("update nginx\n" 0 13 (:parent #175)))) (item (:bullet "+ " :begin 10248 :end 10302 :contents-begin 10256 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10248 :tag nil :mode item :granularity nil :parent #163) 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #142)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #142) #("Guix-notes" 0 10 (:parent #148))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #142))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #139) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #143) #("Guix bioinformatics" 0 19 (:parent #147))) #("and " 0 4 (:parent #143)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #143) #("GNU Guix" 0 8 (:parent #149))) #(".\n" 0 2 (:parent #143))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #139) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #144)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #144) #("GN2 Dependency Graph" 0 20 (:parent #148))) #(".\n" 0 2 (:parent #144))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #137))) :mode nil :granularity nil :parent #131) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #137) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #140) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #143)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #143)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #143))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #138))) :mode nil :granularity nil :parent #131) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #138) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #141) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #144)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #144) #("default" 0 7 (:parent #148)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #148) #("settings.py" 0 11 (:parent #152)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #144))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #141)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #141) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #146))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #141)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #141) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #148))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #139))) :mode nil :granularity nil :parent #131) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #139) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #142) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #145)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #145) #("README" 0 6 (:parent #149))) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #140))) :mode nil :granularity nil :parent #131) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #140) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #143) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #146))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #141))) :mode nil :granularity nil :parent #131) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #144))) :mode section :granularity nil :parent #141) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #144) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #147) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #150))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #147) #("As root configure the Guix profile\n" 0 35 (:parent #151))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #147) #("and run for example\n" 0 20 (:parent #153))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #147)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #147) #("If you want to run as root you may have to set\n" 0 47 (:parent #155))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #147) #("You also need to set\n" 0 21 (:parent #157))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #147) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #159))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #147) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #160))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #147) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #162))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #147) #("When you get errors like:\n" 0 26 (:parent #164))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #147)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #147) #("you may need to set\n" 0 20 (:parent #166))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #145))) :mode nil :granularity nil :parent #141) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #145) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #148) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #151)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #155))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #151) #("s" 0 1 (:parent #156))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #151)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #151) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #151) #("plant" 0 5 (:parent #159))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #151))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #148) #("Download one database from\n" 0 27 (:parent #152))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #148) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #148) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #154))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #148) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #156))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #148)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #148) #("and\n" 0 4 (:parent #159))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #148) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #161))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #148)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #148) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #163))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #148) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #164))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #148) #("Note for the plant database you can rename it to db" 0 51 (:parent #165)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #165) #("webqtl" 0 6 (:parent #169))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #165) #("s" 0 1 (:parent #170))) #(", or\nchange the settings in etc/default" 0 39 (:parent #165)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #165) #("settings.py" 0 11 (:parent #172))) #("to match your path.\n" 0 20 (:parent #165)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #142))) :mode nil :granularity nil :parent #131) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #142) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #145) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #148)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #148)) #("\n" 0 1 (:parent #148))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #145)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #143))) :mode nil :granularity nil :parent #131) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #143) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #146) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #149))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #146) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #144))) :mode nil :granularity nil :parent #131) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #144) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #147) #("See " 0 4 (:parent #150)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #145))) :mode nil :granularity nil :parent #131) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #145) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #148) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #151)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #151))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #146))) :mode nil :granularity nil :parent #131) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #149) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #152) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #155)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #155) #("PATH" 0 4 (:parent #159))) #("and R" 0 5 (:parent #155)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #155) #("LIBS" 0 4 (:parent #161))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #155) #("SITE" 0 4 (:parent #162))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #155))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #152) #("On one system:\n" 0 15 (:parent #157))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #152)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #152) #("and perhaps a few more.\n" 0 24 (:parent #159))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #150)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #150) #("data" 0 4 (:parent #192))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #150)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #150) #("files" 0 5 (:parent #194))) #("/genotype'" 0 10 (:parent #150))) :mode nil :granularity nil :parent #146) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #150) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #153) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #156)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #156) #("data" 0 4 (:parent #160))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #156)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #156) #("settings.py" 0 11 (:parent #162))) #("(see above in\nthis document).\n" 0 30 (:parent #156))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #153) #("You can use the GENENETWORK" 0 27 (:parent #157)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #157) #("FILES" 0 5 (:parent #161))) #("switch to set the datadir, for example\n" 0 39 (:parent #157))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #151))) :mode nil :granularity nil :parent #146) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #151) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #154) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #157))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #152))) :mode nil :granularity nil :parent #146) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #152) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #155) #("This error\n" 0 11 (:parent #158))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #155)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #155) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #160))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #155) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #161)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #161) #("LIBS" 0 4 (:parent #165))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #161) #("SITE" 0 4 (:parent #166))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #161))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #153))) :mode nil :granularity nil :parent #146) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #153) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #156) #("The following error\n" 0 20 (:parent #159))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #156) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #161))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #156)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #156) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #163))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #156)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #156) #("if that works run genenetwork after setting SQL" 0 47 (:parent #165)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #165) #("URI" 0 3 (:parent #169))) #("to something like\n" 0 18 (:parent #165))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #156))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #147))) :mode nil :granularity nil :parent #131) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #150) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #153) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #156))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #153) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #157) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #160) #("Base install\n" 0 13 (:parent #163))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #160) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #167) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #170)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #168) #("Get Guix build going\n" 0 21 (:parent #171))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #168) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #175) #("Build the correct version of Guix\n" 0 34 (:parent #178)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #176) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #179)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #179)) #("\n" 0 1 (:parent #179)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #172) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #177) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #180)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #169) #("Create a gn2 user and home with space\n" 0 38 (:parent #172)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #170) #("Install redis\n" 0 14 (:parent #173))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #170) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #143)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #143) #("Guix-notes" 0 10 (:parent #149))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #143))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #140) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #144) #("Guix bioinformatics" 0 19 (:parent #148))) #("and " 0 4 (:parent #144)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #144) #("GNU Guix" 0 8 (:parent #150))) #(".\n" 0 2 (:parent #144))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #140) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #145)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #145) #("GN2 Dependency Graph" 0 20 (:parent #149))) #(".\n" 0 2 (:parent #145))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #138))) :mode nil :granularity nil :parent #132) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #138) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #141) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #144)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #144)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #144))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #139))) :mode nil :granularity nil :parent #132) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #139) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #142) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #145)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #145) #("default" 0 7 (:parent #149)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #149) #("settings.py" 0 11 (:parent #153)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #145))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #142)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #142) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #147))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #142)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #142) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #149))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #140))) :mode nil :granularity nil :parent #132) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #140) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #143) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #146)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #146) #("README" 0 6 (:parent #150))) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #141))) :mode nil :granularity nil :parent #132) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #141) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #144) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #147))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #142))) :mode nil :granularity nil :parent #132) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #145))) :mode section :granularity nil :parent #142) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #145) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #148) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #151))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #148) #("As root configure the Guix profile\n" 0 35 (:parent #152))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #148) #("and run for example\n" 0 20 (:parent #154))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #148)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #148) #("If you want to run as root you may have to set\n" 0 47 (:parent #156))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #148) #("You also need to set\n" 0 21 (:parent #158))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #148) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #160))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #148) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #161))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #148) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #163))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #148) #("When you get errors like:\n" 0 26 (:parent #165))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #148)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #148) #("you may need to set\n" 0 20 (:parent #167))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #146))) :mode nil :granularity nil :parent #142) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #146) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #149) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #152)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #156))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #152) #("s" 0 1 (:parent #157))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #152)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #152) #("webqtl" 0 6 (:parent #159))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #152) #("plant" 0 5 (:parent #160))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #152))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #149) #("Download one database from\n" 0 27 (:parent #153))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #149) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #149) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #155))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #149) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #157))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #149)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #149) #("and\n" 0 4 (:parent #160))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #149) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #162))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #149)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #149) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #164))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #149) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #165))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #149) #("Note for the plant database you can rename it to db" 0 51 (:parent #166)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #166) #("webqtl" 0 6 (:parent #170))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #166) #("s" 0 1 (:parent #171))) #(", or\nchange the settings in etc/default" 0 39 (:parent #166)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #166) #("settings.py" 0 11 (:parent #173))) #("to match your path.\n" 0 20 (:parent #166)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #143))) :mode nil :granularity nil :parent #132) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #143) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #146) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #149)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #149)) #("\n" 0 1 (:parent #149))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #146)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #144))) :mode nil :granularity nil :parent #132) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #144) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #147) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #150))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #147) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #145))) :mode nil :granularity nil :parent #132) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #145) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #148) #("See " 0 4 (:parent #151)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #(".\n" 0 2 (:parent #151))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #146))) :mode nil :granularity nil :parent #132) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #146) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #149) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #152)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #152))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #147))) :mode nil :granularity nil :parent #132) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #150) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #153) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #156)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #156) #("PATH" 0 4 (:parent #160))) #("and R" 0 5 (:parent #156)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #156) #("LIBS" 0 4 (:parent #162))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #156) #("SITE" 0 4 (:parent #163))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #156))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #153) #("On one system:\n" 0 15 (:parent #158))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #153)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #153) #("and perhaps a few more.\n" 0 24 (:parent #160))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #151)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #151) #("data" 0 4 (:parent #193))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #151)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #151) #("files" 0 5 (:parent #195))) #("/genotype'" 0 10 (:parent #151))) :mode nil :granularity nil :parent #147) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #151) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #154) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #157)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #157) #("data" 0 4 (:parent #161))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #157)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #157) #("settings.py" 0 11 (:parent #163))) #("(see above in\nthis document).\n" 0 30 (:parent #157))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #154) #("You can use the GENENETWORK" 0 27 (:parent #158)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #158) #("FILES" 0 5 (:parent #162))) #("switch to set the datadir, for example\n" 0 39 (:parent #158))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #152))) :mode nil :granularity nil :parent #147) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #152) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #155) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #158))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #153))) :mode nil :granularity nil :parent #147) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #153) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #156) #("This error\n" 0 11 (:parent #159))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #156)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #156) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #161))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #156) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #162)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #162) #("LIBS" 0 4 (:parent #166))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #162) #("SITE" 0 4 (:parent #167))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #162))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #154))) :mode nil :granularity nil :parent #147) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #154) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #157) #("The following error\n" 0 20 (:parent #160))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #157) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #162))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #157)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #157) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #164))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #157)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #157) #("if that works run genenetwork after setting SQL" 0 47 (:parent #166)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #166) #("URI" 0 3 (:parent #170))) #("to something like\n" 0 18 (:parent #166))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #157))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #148))) :mode nil :granularity nil :parent #132) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #151) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #154) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #157))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #172) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #175))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10069 :tag nil :mode item :granularity nil :parent #176) (paragraph (:begin 10079 :end 10097 :contents-begin 10079 :contents-end 10097 :post-blank 0 :post-affiliated 10079 :mode nil :granularity nil :parent #180) #("system stop mysql\n" 0 18 (:parent #183)))) (item (:bullet "- " :begin 10097 :end 10124 :contents-begin 10107 :contents-end 10124 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- 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:commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #138))) :mode nil :granularity nil :parent #133) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #138) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #141) #("Large system deployments can get very " 0 38 (:parent #144)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #144) #("complex" 0 7 (:parent #148))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #144)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #144) #("Guix-notes" 0 10 (:parent #150))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #144))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #141) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #145) #("Guix bioinformatics" 0 19 (:parent #149))) #("and " 0 4 (:parent #145)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #145) #("GNU Guix" 0 8 (:parent #151))) #(".\n" 0 2 (:parent #145))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #141) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #146)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #146) #("GN2 Dependency Graph" 0 20 (:parent #150))) #(".\n" 0 2 (:parent #146))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #139))) :mode nil :granularity nil :parent #133) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #139) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #142) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #145)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #145)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #145))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #140))) :mode nil :granularity nil :parent #133) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #140) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #143) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #146)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #146) #("default" 0 7 (:parent #150)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #150) #("settings.py" 0 11 (:parent #154)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #146))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #143)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #143) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #148))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #143)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #143) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #150))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #141))) :mode nil :granularity nil :parent #133) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #141) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #144) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #147)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #147) #("README" 0 6 (:parent #151))) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #142))) :mode nil :granularity nil :parent #133) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #142) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #145) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #148))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #143))) :mode nil :granularity nil :parent #133) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #146))) :mode section :granularity nil :parent #143) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #146) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #149) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #152))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #149) #("As root configure the Guix profile\n" 0 35 (:parent #153))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #149) #("and run for example\n" 0 20 (:parent #155))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #149)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #149) #("If you want to run as root you may have to set\n" 0 47 (:parent #157))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #149) #("You also need to set\n" 0 21 (:parent #159))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #149) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #161))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #149) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #162))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #149) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #164))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #149) #("When you get errors like:\n" 0 26 (:parent #166))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #149)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #149) #("you may need to set\n" 0 20 (:parent #168))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #147))) :mode nil :granularity nil :parent #143) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #147) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #150) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #153)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #157))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #153) #("s" 0 1 (:parent #158))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #153)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #153) #("webqtl" 0 6 (:parent #160))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #153) #("plant" 0 5 (:parent #161))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #153))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #150) #("Download one database from\n" 0 27 (:parent #154))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #150) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #150) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #156))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #150) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #158))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #150)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #150) #("and\n" 0 4 (:parent #161))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #150) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #163))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #150)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #150) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #165))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #150) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #166))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #150) #("Note for the plant database you can rename it to db" 0 51 (:parent #167)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #167) #("webqtl" 0 6 (:parent #171))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #167) #("s" 0 1 (:parent #172))) #(", or\nchange the settings in etc/default" 0 39 (:parent #167)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #167) #("settings.py" 0 11 (:parent #174))) #("to match your path.\n" 0 20 (:parent #167)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #144))) :mode nil :granularity nil :parent #133) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #144) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #147) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #150)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #150)) #("\n" 0 1 (:parent #150))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #147)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #145))) :mode nil :granularity nil :parent #133) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #145) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #148) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #151))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #148) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #146))) :mode nil :granularity nil :parent #133) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #146) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #149) #("See " 0 4 (:parent #152)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #(".\n" 0 2 (:parent #152))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #147))) :mode nil :granularity nil :parent #133) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #147) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #150) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #153)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #153))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #148))) :mode nil :granularity nil :parent #133) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #151) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #154) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #157)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #157) #("PATH" 0 4 (:parent #161))) #("and R" 0 5 (:parent #157)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #157) #("LIBS" 0 4 (:parent #163))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #157) #("SITE" 0 4 (:parent #164))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #157))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #154) #("On one system:\n" 0 15 (:parent #159))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #154)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #154) #("and perhaps a few more.\n" 0 24 (:parent #161))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #152)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #152) #("data" 0 4 (:parent #194))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #152)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #152) #("files" 0 5 (:parent #196))) #("/genotype'" 0 10 (:parent #152))) :mode nil :granularity nil :parent #148) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #152) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #155) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #158)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #158) #("data" 0 4 (:parent #162))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #158)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #158) #("settings.py" 0 11 (:parent #164))) #("(see above in\nthis document).\n" 0 30 (:parent #158))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #155) #("You can use the GENENETWORK" 0 27 (:parent #159)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #159) #("FILES" 0 5 (:parent #163))) #("switch to set the datadir, for example\n" 0 39 (:parent #159))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #155)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #153))) :mode nil :granularity nil :parent #148) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #153) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #156) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #159))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #154))) :mode nil :granularity nil :parent #148) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #154) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #157) #("This error\n" 0 11 (:parent #160))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #157)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #157) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #162))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #157) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #163)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #163) #("LIBS" 0 4 (:parent #167))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #163) #("SITE" 0 4 (:parent #168))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #163))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #155))) :mode nil :granularity nil :parent #148) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #155) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #158) #("The following error\n" 0 20 (:parent #161))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #158) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #163))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #158)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #158) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #165))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #158)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #158) #("if that works run genenetwork after setting SQL" 0 47 (:parent #167)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #167) #("URI" 0 3 (:parent #171))) #("to something like\n" 0 18 (:parent #167))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #158))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #149))) :mode nil :granularity nil :parent #133) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #152))) :mode section :granularity nil :parent #149) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #152) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #155) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #158))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #155) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #159) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #162) #("Base install\n" 0 13 (:parent #165))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #162) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #166) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #169) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #172)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #166) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #170) #("Get Guix build going\n" 0 21 (:parent #173))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #170) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #174) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #177) #("Build the correct version of Guix\n" 0 34 (:parent #180)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #174) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #178) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #181)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #181)) #("\n" 0 1 (:parent #181)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #174) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #179) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #182)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #166) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #171) #("Create a gn2 user and home with space\n" 0 38 (:parent #174)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #166) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #172) #("Install redis\n" 0 14 (:parent #175))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #172) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #176) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #179) #("add to systemd\n" 0 15 (:parent #182)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 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 #145)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #145) #("Guix-notes" 0 10 (:parent #151))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #145))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #142) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #146) #("Guix bioinformatics" 0 19 (:parent #150))) #("and " 0 4 (:parent #146)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #146) #("GNU Guix" 0 8 (:parent #152))) #(".\n" 0 2 (:parent #146))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #142) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #147)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #147) #("GN2 Dependency Graph" 0 20 (:parent #151))) #(".\n" 0 2 (:parent #147))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #140))) :mode nil :granularity nil :parent #134) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #140) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #143) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #146)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #146)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #146))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #141))) :mode nil :granularity nil :parent #134) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #141) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #144) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #147)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #147) #("default" 0 7 (:parent #151)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #151) #("settings.py" 0 11 (:parent #155)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #147))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #144)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #144) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #149))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #144)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #144) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #151))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #142))) :mode nil :granularity nil :parent #134) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #142) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #145) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #148)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #148) #("README" 0 6 (:parent #152))) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #143))) :mode nil :granularity nil :parent #134) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #143) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #146) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #149))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #144))) :mode nil :granularity nil :parent #134) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #147))) :mode section :granularity nil :parent #144) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #147) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #150) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #153))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #150) #("As root configure the Guix profile\n" 0 35 (:parent #154))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #150) #("and run for example\n" 0 20 (:parent #156))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #150)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #150) #("If you want to run as root you may have to set\n" 0 47 (:parent #158))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #150) #("You also need to set\n" 0 21 (:parent #160))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #150) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #162))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #150) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #163))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #150) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #165))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #150) #("When you get errors like:\n" 0 26 (:parent #167))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #150)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #150) #("you may need to set\n" 0 20 (:parent #169))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #148))) :mode nil :granularity nil :parent #144) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #148) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #151) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #154)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #158))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #154) #("s" 0 1 (:parent #159))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #154)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #154) #("webqtl" 0 6 (:parent #161))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #154) #("plant" 0 5 (:parent #162))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #154))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #151) #("Download one database from\n" 0 27 (:parent #155))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #151) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #151) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #157))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #151) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #159))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #151)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #151) #("and\n" 0 4 (:parent #162))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #151) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #164))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #151)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #151) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #166))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #151) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #167))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #151) #("Note for the plant database you can rename it to db" 0 51 (:parent #168)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #168) #("webqtl" 0 6 (:parent #172))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #168) #("s" 0 1 (:parent #173))) #(", or\nchange the settings in etc/default" 0 39 (:parent #168)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #168) #("settings.py" 0 11 (:parent #175))) #("to match your path.\n" 0 20 (:parent #168)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #145))) :mode nil :granularity nil :parent #134) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #145) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #148) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #151)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #151)) #("\n" 0 1 (:parent #151))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #148)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #146))) :mode nil :granularity nil :parent #134) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #146) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #149) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #152))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #149) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #147))) :mode nil :granularity nil :parent #134) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #147) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #150) #("See " 0 4 (:parent #153)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #(".\n" 0 2 (:parent #153))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #148))) :mode nil :granularity nil :parent #134) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #148) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #151) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #154)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #154))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #149))) :mode nil :granularity nil :parent #134) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #152))) :mode section :granularity nil :parent #149) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #152) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #155) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #158)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #158) #("PATH" 0 4 (:parent #162))) #("and R" 0 5 (:parent #158)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #158) #("LIBS" 0 4 (:parent #164))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #158) #("SITE" 0 4 (:parent #165))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #158))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #155) #("On one system:\n" 0 15 (:parent #160))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #155)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #155) #("and perhaps a few more.\n" 0 24 (:parent #162))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #153)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #153) #("data" 0 4 (:parent #195))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #153)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #153) #("files" 0 5 (:parent #197))) #("/genotype'" 0 10 (:parent #153))) :mode nil :granularity nil :parent #149) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #153) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #156) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #159)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #159) #("data" 0 4 (:parent #163))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #159)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #159) #("settings.py" 0 11 (:parent #165))) #("(see above in\nthis document).\n" 0 30 (:parent #159))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #156) #("You can use the GENENETWORK" 0 27 (:parent #160)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #160) #("FILES" 0 5 (:parent #164))) #("switch to set the datadir, for example\n" 0 39 (:parent #160))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #156)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #154))) :mode nil :granularity nil :parent #149) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #154) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #157) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #160))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #155))) :mode nil :granularity nil :parent #149) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #155) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #158) #("This error\n" 0 11 (:parent #161))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #158)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #158) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #163))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #158) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #164)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #164) #("LIBS" 0 4 (:parent #168))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #164) #("SITE" 0 4 (:parent #169))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #164))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #156))) :mode nil :granularity nil :parent #149) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #156) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #159) #("The following error\n" 0 20 (:parent #162))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #159) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #164))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #159)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #159) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #166))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #159)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #159) #("if that works run genenetwork after setting SQL" 0 47 (:parent #168)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #168) #("URI" 0 3 (:parent #172))) #("to something like\n" 0 18 (:parent #168))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #159))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #150))) :mode nil :granularity nil :parent #134) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #153))) :mode section :granularity nil :parent #150) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #153) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #156) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #159))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #156) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #160) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #163) #("Base install\n" 0 13 (:parent #166))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #163) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #167) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #170) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #173)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #167) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #171) #("Get Guix build going\n" 0 21 (:parent #174))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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nil :mode item :granularity nil :parent #181) (paragraph (:begin 10287 :end 10302 :contents-begin 10287 :contents-end 10302 :post-blank 0 :post-affiliated 10287 :mode nil :granularity nil :parent #184) #("add to systemd\n" 0 15 (:parent #187)))))))))))))) #64)) #40)) . #0)) (paragraph (:begin 523 :end 571 :contents-begin 523 :contents-end 571 :post-blank 0 :post-affiliated 523 :mode nil :granularity nil :parent #8) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 523 :end 570 :contents-begin 548 :contents-end 568 :post-blank 0 :parent #11) #("GN2 Dependency Graph" 0 20 (:parent #14))) #("\n" 0 1 (:parent #11)))) (item (:bullet "- " :begin 571 :end 646 :contents-begin 574 :contents-end 646 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 249) (249 1 "- " nil nil nil 278) (278 1 "- " nil nil 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:path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #135) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #138))) #89 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #140))) :mode nil :granularity nil :parent #135) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #140) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #143) #("Large system deployments can get very " 0 38 (:parent #146)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #146) #("complex" 0 7 (:parent #150))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #146)) (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 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #146) #("Guix-notes" 0 10 (:parent #152))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #146))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #143) #("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 #147)) (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 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #147) #("Guix bioinformatics" 0 19 (:parent #151))) #("and " 0 4 (:parent #147)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #147) #("GNU Guix" 0 8 (:parent #153))) #(".\n" 0 2 (:parent #147))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #143) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #148)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #148) #("GN2 Dependency Graph" 0 20 (:parent #152))) #(".\n" 0 2 (:parent #148))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #141))) :mode nil :granularity nil :parent #135) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #141) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #144) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #147)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #147)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #147))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #142))) :mode nil :granularity nil :parent #135) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #142) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #145) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #148)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #148) #("default" 0 7 (:parent #152)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #152) #("settings.py" 0 11 (:parent #156)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #148))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #145)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #145) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #150))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #145)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #145) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #152))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #143))) :mode nil :granularity nil :parent #135) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #143) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #146) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #149)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #149) #("README" 0 6 (:parent #153))) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #144))) :mode nil :granularity nil :parent #135) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #144) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #147) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #150))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #145))) :mode nil :granularity nil :parent #135) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #148))) :mode section :granularity nil :parent #145) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #148) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #151) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #154))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #151) #("As root configure the Guix profile\n" 0 35 (:parent #155))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #151)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #151) #("and run for example\n" 0 20 (:parent #157))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #151)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #151) #("If you want to run as root you may have to set\n" 0 47 (:parent #159))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #151) #("You also need to set\n" 0 21 (:parent #161))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #151) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #163))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #151) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #164))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #151) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #166))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #151) #("When you get errors like:\n" 0 26 (:parent #168))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #151)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #151) #("you may need to set\n" 0 20 (:parent #170))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #149))) :mode nil :granularity nil :parent #145) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #149) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #152) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #155)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #155) #("webqtl" 0 6 (:parent #159))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #155) #("s" 0 1 (:parent #160))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #155)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #155) #("webqtl" 0 6 (:parent #162))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #155) #("plant" 0 5 (:parent #163))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #155))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #152) #("Download one database from\n" 0 27 (:parent #156))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #152) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #152) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #158))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #152) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #160))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #152)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #152) #("and\n" 0 4 (:parent #163))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #152) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #165))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #152)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #152) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #167))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #152) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #168))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #152) #("Note for the plant database you can rename it to db" 0 51 (:parent #169)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #(", or\nchange the settings in etc/default" 0 39 (:parent #169)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #169) #("settings.py" 0 11 (:parent #176))) #("to match your path.\n" 0 20 (:parent #169)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #146))) :mode nil :granularity nil :parent #135) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #146) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #149) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #152)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #152)) #("\n" 0 1 (:parent #152))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #149)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #147))) :mode nil :granularity nil :parent #135) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #147) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #150) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #153))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #150) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #148))) :mode nil :granularity nil :parent #135) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #148) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #151) #("See " 0 4 (:parent #154)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #(".\n" 0 2 (:parent #154))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #149))) :mode nil :granularity nil :parent #135) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #149) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #152) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #155)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #155))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #150))) :mode nil :granularity nil :parent #135) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #153))) :mode section :granularity nil :parent #150) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #153) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #156) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #159)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #159) #("PATH" 0 4 (:parent #163))) #("and R" 0 5 (:parent #159)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #159) #("LIBS" 0 4 (:parent #165))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #159) #("SITE" 0 4 (:parent #166))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #159))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #156) #("On one system:\n" 0 15 (:parent #161))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #156)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #156) #("and perhaps a few more.\n" 0 24 (:parent #163))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #154)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #154) #("data" 0 4 (:parent #196))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #154)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #154) #("files" 0 5 (:parent #198))) #("/genotype'" 0 10 (:parent #154))) :mode nil :granularity nil :parent #150) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #154) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #157) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #160)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #160) #("data" 0 4 (:parent #164))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #160)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #160) #("settings.py" 0 11 (:parent #166))) #("(see above in\nthis document).\n" 0 30 (:parent #160))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #157) #("You can use the GENENETWORK" 0 27 (:parent #161)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #161) #("FILES" 0 5 (:parent #165))) #("switch to set the datadir, for example\n" 0 39 (:parent #161))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #157)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #155))) :mode nil :granularity nil :parent #150) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #155) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #158) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #161))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #156))) :mode nil :granularity nil :parent #150) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #156) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #159) #("This error\n" 0 11 (:parent #162))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #159)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #159) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #164))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #159) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #165)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #165) #("LIBS" 0 4 (:parent #169))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #165) #("SITE" 0 4 (:parent #170))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #165))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #157))) :mode nil :granularity nil :parent #150) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #157) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #160) #("The following error\n" 0 20 (:parent #163))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #160)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #160) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #165))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #160)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #160) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #167))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #160)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #160) #("if that works run genenetwork after setting SQL" 0 47 (:parent #169)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #169) #("URI" 0 3 (:parent #173))) #("to something like\n" 0 18 (:parent #169))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #160))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #151))) :mode nil :granularity nil :parent #135) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #154))) :mode section :granularity nil :parent #151) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #154) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #157) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #160))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #164) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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nil :parent #177) #("update nginx\n" 0 13 (:parent #180)))) (item (:bullet "+ " :begin 10248 :end 10302 :contents-begin 10256 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10248 :tag nil :mode item :granularity nil :parent #168) 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nil :mode item :granularity nil :parent #182) (paragraph (:begin 10287 :end 10302 :contents-begin 10287 :contents-end 10302 :post-blank 0 :post-affiliated 10287 :mode nil :granularity nil :parent #185) #("add to systemd\n" 0 15 (:parent #188)))))))))))))) #65)) #41)) . #0)) (paragraph (:begin 574 :end 646 :contents-begin 574 :contents-end 646 :post-blank 0 :post-affiliated 574 :mode nil :granularity nil :parent #9) (link (:type "custom-id" :path "working-with-the-gn2-source-code" :format bracket :raw-link "#working-with-the-gn2-source-code" :application nil :search-option nil :begin 574 :end 645 :contents-begin 611 :contents-end 643 :post-blank 0 :parent #12) #("Working with the GN2 source code" 0 32 (:parent #15))) #("\n" 0 1 (:parent #12)))) (item (:bullet "- " :begin 646 :end 675 :contents-begin 649 :contents-end 675 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 181) (181 1 "- " nil nil nil 214) (214 1 "- " nil nil nil 249) (249 1 "- " 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:granularity nil :parent #141) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #144) #("Large system deployments can get very " 0 38 (:parent #147)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #147) #("complex" 0 7 (:parent #151))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #147)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #147) #("Guix-notes" 0 10 (:parent #153))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #147))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #144) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #148) #("Guix bioinformatics" 0 19 (:parent #152))) #("and " 0 4 (:parent #148)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #148) #("GNU Guix" 0 8 (:parent #154))) #(".\n" 0 2 (:parent #148))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #144) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #149)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #149) #("GN2 Dependency Graph" 0 20 (:parent #153))) #(".\n" 0 2 (:parent #149))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #142))) :mode nil :granularity nil :parent #136) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #142) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #145) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #148)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #148)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #148))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #143))) :mode nil :granularity nil :parent #136) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #143) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #146) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #149)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #149) #("default" 0 7 (:parent #153)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #153) #("settings.py" 0 11 (:parent #157)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #149))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #146)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #146) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #151))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #146)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #146) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #153))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #144))) :mode nil :granularity nil :parent #136) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #144) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #147) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #150)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #150) #("README" 0 6 (:parent #154))) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #145))) :mode nil :granularity nil :parent #136) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #145) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #148) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #151))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #146))) :mode nil :granularity nil :parent #136) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #149))) :mode section :granularity nil :parent #146) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #149) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #152) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #155))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #152) #("As root configure the Guix profile\n" 0 35 (:parent #156))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #152)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #152) #("and run for example\n" 0 20 (:parent #158))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #152)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #152) #("If you want to run as root you may have to set\n" 0 47 (:parent #160))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #152)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #152) #("You also need to set\n" 0 21 (:parent #162))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #152)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #152) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #164))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #152) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #165))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #152)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #152) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #167))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #152)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #152) #("When you get errors like:\n" 0 26 (:parent #169))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #152)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #152) #("you may need to set\n" 0 20 (:parent #171))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #150))) :mode nil :granularity nil :parent #146) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #150) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #153) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #156)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #156) #("webqtl" 0 6 (:parent #160))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #156) #("s" 0 1 (:parent #161))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #156)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #156) #("webqtl" 0 6 (:parent #163))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #156) #("plant" 0 5 (:parent #164))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #156))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #153) #("Download one database from\n" 0 27 (:parent #157))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #153) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #("\n" 0 1 (:parent #158))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #153) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #159))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #153)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #153) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #161))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #153)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #153)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #153) #("and\n" 0 4 (:parent #164))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #153)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #153) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #166))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #153)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #153) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #168))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #153) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #169))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #153) #("Note for the plant database you can rename it to db" 0 51 (:parent #170)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #170) #("webqtl" 0 6 (:parent #174))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #170) #("s" 0 1 (:parent #175))) #(", or\nchange the settings in etc/default" 0 39 (:parent #170)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #170) #("settings.py" 0 11 (:parent #177))) #("to match your path.\n" 0 20 (:parent #170)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #147))) :mode nil :granularity nil :parent #136) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #147) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #150) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #153)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #153)) #("\n" 0 1 (:parent #153))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #150)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #148))) :mode nil :granularity nil :parent #136) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #148) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #151) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #154))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #151) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #149))) :mode nil :granularity nil :parent #136) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #149) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #152) #("See " 0 4 (:parent #155)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #(".\n" 0 2 (:parent #155))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #150))) :mode nil :granularity nil :parent #136) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #150) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #153) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #156)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #156))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #151))) :mode nil :granularity nil :parent #136) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #154))) :mode section :granularity nil :parent #151) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #154) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #157) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #160)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #160) #("PATH" 0 4 (:parent #164))) #("and R" 0 5 (:parent #160)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #160) #("LIBS" 0 4 (:parent #166))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #160) #("SITE" 0 4 (:parent #167))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #160))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #157) #("On one system:\n" 0 15 (:parent #162))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #157)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #157) #("and perhaps a few more.\n" 0 24 (:parent #164))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #155)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #155) #("data" 0 4 (:parent #197))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #155)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #155) #("files" 0 5 (:parent #199))) #("/genotype'" 0 10 (:parent #155))) :mode nil :granularity nil :parent #151) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #155) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #158) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #161)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #161) #("data" 0 4 (:parent #165))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #161)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #161) #("settings.py" 0 11 (:parent #167))) #("(see above in\nthis document).\n" 0 30 (:parent #161))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #158) #("You can use the GENENETWORK" 0 27 (:parent #162)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #162) #("FILES" 0 5 (:parent #166))) #("switch to set the datadir, for example\n" 0 39 (:parent #162))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #158)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #156) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #159) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #162))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #157) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #160) #("This error\n" 0 11 (:parent #163))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #160)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #160) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #165))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #160) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #166)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #166) #("LIBS" 0 4 (:parent #170))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #166) #("SITE" 0 4 (:parent #171))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #166))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #158) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #161) #("The following error\n" 0 20 (:parent #164))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #161)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #161) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #166))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #161)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #161) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #168))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #161)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #161) #("if that works run genenetwork after setting SQL" 0 47 (:parent #170)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #170) #("URI" 0 3 (:parent #174))) #("to something like\n" 0 18 (:parent #170))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #161))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #152))) :mode nil :granularity nil :parent #136) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #155) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #158) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #161))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #158) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #162) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #165) #("Base install\n" 0 13 (:parent #168))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #165) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #172) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #175)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #173) #("Get Guix build going\n" 0 21 (:parent #176))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #173) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #177) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #180) #("Build the correct version of Guix\n" 0 34 (:parent #183)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #177) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #181) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #184)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #184)) #("\n" 0 1 (:parent #184)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #177) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #182) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #185)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #174) #("Create a gn2 user and home with space\n" 0 38 (:parent #177)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #169) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #175) #("Install redis\n" 0 14 (:parent #178))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #175) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #148)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #148) #("Guix-notes" 0 10 (:parent #154))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #148))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #145) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #149)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #149) #("Guix bioinformatics" 0 19 (:parent #153))) #("and " 0 4 (:parent #149)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #149) #("GNU Guix" 0 8 (:parent #155))) #(".\n" 0 2 (:parent #149))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #145) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #150)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #150) #("GN2 Dependency Graph" 0 20 (:parent #154))) #(".\n" 0 2 (:parent #150))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #143))) :mode nil :granularity nil :parent #137) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #143) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #146) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #149)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #149)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #149))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #144))) :mode nil :granularity nil :parent #137) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #144) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #147) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #150)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #150) #("default" 0 7 (:parent #154)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #154) #("settings.py" 0 11 (:parent #158)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #150))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #147)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #147) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #152))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #147)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #147) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #154))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #145))) :mode nil :granularity nil :parent #137) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #145) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #148) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #151)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #151) #("README" 0 6 (:parent #155))) #(".\n" 0 2 (:parent #151))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #146))) :mode nil :granularity nil :parent #137) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #146) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #149) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #152))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #147))) :mode nil :granularity nil :parent #137) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #150))) :mode section :granularity nil :parent #147) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #150) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #153) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #156))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #153) #("As root configure the Guix profile\n" 0 35 (:parent #157))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #153)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #153) #("and run for example\n" 0 20 (:parent #159))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #153)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #153) #("If you want to run as root you may have to set\n" 0 47 (:parent #161))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #153)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #153) #("You also need to set\n" 0 21 (:parent #163))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #153)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #153) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #165))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #153) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #166))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #153)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #153) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #168))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #153)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #153) #("When you get errors like:\n" 0 26 (:parent #170))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #153)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #153) #("you may need to set\n" 0 20 (:parent #172))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #153)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #151))) :mode nil :granularity nil :parent #147) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #151) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #154) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #157)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #157) #("webqtl" 0 6 (:parent #161))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #157) #("s" 0 1 (:parent #162))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #157)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #157) #("webqtl" 0 6 (:parent #164))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #157) #("plant" 0 5 (:parent #165))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #157))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #154) #("Download one database from\n" 0 27 (:parent #158))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #154) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #159)) #("\n" 0 1 (:parent #159))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #154) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #160))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #154)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #154) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #162))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #154)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #154)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #154) #("and\n" 0 4 (:parent #165))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #154)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #154) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #167))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #154)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #154) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #169))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #154) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #170))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #154) #("Note for the plant database you can rename it to db" 0 51 (:parent #171)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #171) #("webqtl" 0 6 (:parent #175))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #171) #("s" 0 1 (:parent #176))) #(", or\nchange the settings in etc/default" 0 39 (:parent #171)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #171) #("settings.py" 0 11 (:parent #178))) #("to match your path.\n" 0 20 (:parent #171)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #148))) :mode nil :granularity nil :parent #137) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #148) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #151) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #154)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #154)) #("\n" 0 1 (:parent #154))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #151)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #149))) :mode nil :granularity nil :parent #137) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #149) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #152) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #155))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #152) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #("\n" 0 1 (:parent #156))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #150))) :mode nil :granularity nil :parent #137) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #150) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #153) #("See " 0 4 (:parent #156)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #156)) #(".\n" 0 2 (:parent #156))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #151))) :mode nil :granularity nil :parent #137) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #151) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #154) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #157)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #157))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #152))) :mode nil :granularity nil :parent #137) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #155))) :mode section :granularity nil :parent #152) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #155) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #158) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #161)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #161) #("PATH" 0 4 (:parent #165))) #("and R" 0 5 (:parent #161)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #161) #("LIBS" 0 4 (:parent #167))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #161) #("SITE" 0 4 (:parent #168))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #161))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #158) #("On one system:\n" 0 15 (:parent #163))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #158)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #158) #("and perhaps a few more.\n" 0 24 (:parent #165))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #156)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #156) #("data" 0 4 (:parent #198))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #156)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #156) #("files" 0 5 (:parent #200))) #("/genotype'" 0 10 (:parent #156))) :mode nil :granularity nil :parent #152) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #156) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #159) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #162)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #162) #("data" 0 4 (:parent #166))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #162)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #162) #("settings.py" 0 11 (:parent #168))) #("(see above in\nthis document).\n" 0 30 (:parent #162))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #159) #("You can use the GENENETWORK" 0 27 (:parent #163)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #163) #("FILES" 0 5 (:parent #167))) #("switch to set the datadir, for example\n" 0 39 (:parent #163))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #159)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #157))) :mode nil :granularity nil :parent #152) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #157) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #160) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #163))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #158))) :mode nil :granularity nil :parent #152) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #158) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #161) #("This error\n" 0 11 (:parent #164))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #161)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #161) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #166))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #161) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #167)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #167) #("LIBS" 0 4 (:parent #171))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #167) #("SITE" 0 4 (:parent #172))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #167))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #159))) :mode nil :granularity nil :parent #152) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #159) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #162) #("The following error\n" 0 20 (:parent #165))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #162)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #162) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #167))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #162)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #162) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #169))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #162)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #162) #("if that works run genenetwork after setting SQL" 0 47 (:parent #171)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #171) #("URI" 0 3 (:parent #175))) #("to something like\n" 0 18 (:parent #171))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #162))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #153))) :mode nil :granularity nil :parent #137) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #156))) :mode section :granularity nil :parent #153) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #156) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #159) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #162))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #177) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #180))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10069 :tag nil :mode item :granularity nil :parent #181) (paragraph (:begin 10079 :end 10097 :contents-begin 10079 :contents-end 10097 :post-blank 0 :post-affiliated 10079 :mode nil :granularity nil :parent #185) #("system stop mysql\n" 0 18 (:parent #188)))) (item (:bullet "- " :begin 10097 :end 10124 :contents-begin 10107 :contents-end 10124 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- 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Follow the instructions on\n" 0 117 (:parent #150)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #150)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #150))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #145))) :mode nil :granularity nil :parent #138) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #145) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #148) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #151)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #151) #("default" 0 7 (:parent #155)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #155) #("settings.py" 0 11 (:parent #159)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #151))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #148)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #148) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #153))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #148)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #148) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #155))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #146))) :mode nil :granularity nil :parent #138) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #146) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #149) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #152)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #152) #("README" 0 6 (:parent #156))) #(".\n" 0 2 (:parent #152))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #147))) :mode nil :granularity nil :parent #138) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #147) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #150) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #153))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #148))) :mode nil :granularity nil :parent #138) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #151))) :mode section :granularity nil :parent #148) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #151) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #154) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #157))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #154) #("As root configure the Guix profile\n" 0 35 (:parent #158))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #154)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #154) #("and run for example\n" 0 20 (:parent #160))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #154)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #154) #("If you want to run as root you may have to set\n" 0 47 (:parent #162))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #154)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #154) #("You also need to set\n" 0 21 (:parent #164))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #154)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #154) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #166))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #154) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #167))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #154)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #154) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #169))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #154)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #154) #("When you get errors like:\n" 0 26 (:parent #171))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #154)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #154) #("you may need to set\n" 0 20 (:parent #173))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #154)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #152))) :mode nil :granularity nil :parent #148) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #152) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #155) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #158)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #158) #("webqtl" 0 6 (:parent #162))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #158) #("s" 0 1 (:parent #163))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #158)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #158) #("webqtl" 0 6 (:parent #165))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #158) #("plant" 0 5 (:parent #166))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #158))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #155) #("Download one database from\n" 0 27 (:parent #159))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #155) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #160)) #("\n" 0 1 (:parent #160))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #155) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #161))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #155)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #155) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #163))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #155)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #155)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #155) #("and\n" 0 4 (:parent #166))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #155)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #155) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #168))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #155)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #155) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #170))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #155) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #171))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #155) #("Note for the plant database you can rename it to db" 0 51 (:parent #172)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #172) #("webqtl" 0 6 (:parent #176))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #172) #("s" 0 1 (:parent #177))) #(", or\nchange the settings in etc/default" 0 39 (:parent #172)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #172) #("settings.py" 0 11 (:parent #179))) #("to match your path.\n" 0 20 (:parent #172)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #149))) :mode nil :granularity nil :parent #138) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #149) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #152) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #155)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #155)) #("\n" 0 1 (:parent #155))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #152)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #150))) :mode nil :granularity nil :parent #138) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #150) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #153) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #156))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #153) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #("\n" 0 1 (:parent #157))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #151))) :mode nil :granularity nil :parent #138) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #151) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #154) #("See " 0 4 (:parent #157)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #157)) #(".\n" 0 2 (:parent #157))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #152))) :mode nil :granularity nil :parent #138) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #152) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #155) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #158)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #158)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #158))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #153))) :mode nil :granularity nil :parent #138) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #156))) :mode section :granularity nil :parent #153) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #156) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #159) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #162)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #162) #("PATH" 0 4 (:parent #166))) #("and R" 0 5 (:parent #162)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #162) #("LIBS" 0 4 (:parent #168))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #162) #("SITE" 0 4 (:parent #169))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #162))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #159)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #159) #("On one system:\n" 0 15 (:parent #164))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #159)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #159) #("and perhaps a few more.\n" 0 24 (:parent #166))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #157)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #157) #("data" 0 4 (:parent #199))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #157)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #157) #("files" 0 5 (:parent #201))) #("/genotype'" 0 10 (:parent #157))) :mode nil :granularity nil :parent #153) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #157) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #160) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #163)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #163) #("data" 0 4 (:parent #167))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #163)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #163) #("settings.py" 0 11 (:parent #169))) #("(see above in\nthis document).\n" 0 30 (:parent #163))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #160) #("You can use the GENENETWORK" 0 27 (:parent #164)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #164) #("FILES" 0 5 (:parent #168))) #("switch to set the datadir, for example\n" 0 39 (:parent #164))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #160)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #158))) :mode nil :granularity nil :parent #153) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #158) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #161) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #164))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #159))) :mode nil :granularity nil :parent #153) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #159) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #162) #("This error\n" 0 11 (:parent #165))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #162)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #162) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #167))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #162) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #168)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #168) #("LIBS" 0 4 (:parent #172))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #168) #("SITE" 0 4 (:parent #173))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #168))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #160))) :mode nil :granularity nil :parent #153) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #160) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #163) #("The following error\n" 0 20 (:parent #166))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #163)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #163) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #168))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #163)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #163) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #170))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #163)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #163) #("if that works run genenetwork after setting SQL" 0 47 (:parent #172)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #172) #("URI" 0 3 (:parent #176))) #("to something like\n" 0 18 (:parent #172))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #163))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #154))) :mode nil :granularity nil :parent #138) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #157))) :mode section :granularity nil :parent #154) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #157) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #160) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #163))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #160) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #164) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #167) #("Base install\n" 0 13 (:parent #170))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #167) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #174) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #177)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #171) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #175) #("Get Guix build going\n" 0 21 (:parent #178))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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:post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #48))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #94) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #99) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #102) #("Large system deployments can get very " 0 38 (:parent #105)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #105) #("complex" 0 7 (:parent #109))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #111))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #106) #("GNU Guix" 0 8 (:parent #112))) #(".\n" 0 2 (:parent #106))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #102) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #107)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #107) #("GN2 Dependency Graph" 0 20 (:parent #111))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #100))) :mode nil :granularity nil :parent #94) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #100) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #103) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #106)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #106)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #106))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #101) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #104) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #107)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #107) #("default" 0 7 (:parent #111)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #111) #("settings.py" 0 11 (:parent #115)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #107))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #104) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #109))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #104) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #111))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #102))) :mode nil :granularity nil :parent #94) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #102) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #105) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #108)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #108) #("README" 0 6 (:parent #112))) #(".\n" 0 2 (:parent #108))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #103) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #106) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #109))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #104))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #107))) :mode section :granularity nil :parent #104) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #107) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #110) #("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 #113))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #110) #("As root configure the Guix profile\n" 0 35 (:parent #114))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #110)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #110) #("and run for example\n" 0 20 (:parent #116))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #110)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #110) #("If you want to run as root you may have to set\n" 0 47 (:parent #118))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #110) #("You also need to set\n" 0 21 (:parent #120))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #110) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #122))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #110) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #123))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #110) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #125))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #110) #("When you get errors like:\n" 0 26 (:parent #127))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #110) #("you may need to set\n" 0 20 (:parent #129))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #110)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #108))) :mode nil :granularity nil :parent #104) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #108) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #111) #("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 #114)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #114) #("webqtl" 0 6 (:parent #118))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #114) #("s" 0 1 (:parent #119))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #114)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #114) #("webqtl" 0 6 (:parent #121))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #114) #("plant" 0 5 (:parent #122))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #114))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #111) #("Download one database from\n" 0 27 (:parent #115))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #111) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\n" 0 1 (:parent #116))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #111) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #117))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #111) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #119))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #111)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #111) #("and\n" 0 4 (:parent #122))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #111) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #124))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #111) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #126))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #111) #("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 #127))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #111) #("Note for the plant database you can rename it to db" 0 51 (:parent #128)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #128) #("webqtl" 0 6 (:parent #132))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #128) #("s" 0 1 (:parent #133))) #(", or\nchange the settings in etc/default" 0 39 (:parent #128)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #128) #("settings.py" 0 11 (:parent #135))) #("to match your path.\n" 0 20 (:parent #128)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #105) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #108) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #111)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #("\n" 0 1 (:parent #111))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #108)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #106))) :mode nil :granularity nil :parent #94) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #106) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #109) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #112))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #109) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #("\n" 0 1 (:parent #113))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #107) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #110) #("See " 0 4 (:parent #113)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #(".\n" 0 2 (:parent #113))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #108))) :mode nil :granularity nil :parent #94) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #108) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #111) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #114)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #114))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #109))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #112))) :mode section :granularity nil :parent #109) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #112) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #115) #("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 #118)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #118) #("PATH" 0 4 (:parent #122))) #("and R" 0 5 (:parent #118)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #118) #("LIBS" 0 4 (:parent #124))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #118) #("SITE" 0 4 (:parent #125))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #118))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #115) #("On one system:\n" 0 15 (:parent #120))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #115) #("and perhaps a few more.\n" 0 24 (:parent #122))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #113)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #113) #("data" 0 4 (:parent #155))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #113)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #113) #("files" 0 5 (:parent #157))) #("/genotype'" 0 10 (:parent #113))) :mode nil :granularity nil :parent #109) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #113) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #116) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #119)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #119) #("data" 0 4 (:parent #123))) #(". 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 #119)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #119) #("settings.py" 0 11 (:parent #125))) #("(see above in\nthis document).\n" 0 30 (:parent #119))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #116) #("You can use the GENENETWORK" 0 27 (:parent #120)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #120) #("FILES" 0 5 (:parent #124))) #("switch to set the datadir, for example\n" 0 39 (:parent #120))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #116)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #114))) :mode nil :granularity nil :parent #109) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #114) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #117) #("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 #120))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #115))) :mode nil :granularity nil :parent #109) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #115) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #118) #("This error\n" 0 11 (:parent #121))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #118)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #118) #("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 #123))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #118) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #124)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #124) #("LIBS" 0 4 (:parent #128))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #124) #("SITE" 0 4 (:parent #129))) #(". 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 #124))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #116))) :mode nil :granularity nil :parent #109) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #116) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #119) #("The following error\n" 0 20 (:parent #122))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #119)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #119) #("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 #124))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #119)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #119) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #126))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #119)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #119) #("if that works run genenetwork after setting SQL" 0 47 (:parent #128)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #128) #("URI" 0 3 (:parent #132))) #("to something like\n" 0 18 (:parent #128))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #119))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #110))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #113))) :mode section :granularity nil :parent #110) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #113) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #116) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #119))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #123) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " 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 #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. 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Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #360) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #367) #("Base install\n" 0 13 (:parent #370))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #374) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #377)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #375) #("Get Guix build going\n" 0 21 (:parent #378))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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:robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #94) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #97))) #48 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #99))) :mode nil :granularity nil :parent #94) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #99) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #102) #("Large system deployments can get very " 0 38 (:parent #105)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #105) #("complex" 0 7 (:parent #109))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #105)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #105) #("Guix-notes" 0 10 (:parent #111))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #105))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #102) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #106) #("Guix bioinformatics" 0 19 (:parent #110))) #("and " 0 4 (:parent #106)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #106) #("GNU Guix" 0 8 (:parent #112))) #(".\n" 0 2 (:parent #106))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #102) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #107)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #107) #("GN2 Dependency Graph" 0 20 (:parent #111))) #(".\n" 0 2 (:parent #107))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #100))) :mode nil :granularity nil :parent #94) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #100) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #103) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #106)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #106)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #106))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #101))) :mode nil :granularity nil :parent #94) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #101) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #104) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #107)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #107) #("default" 0 7 (:parent #111)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #111) #("settings.py" 0 11 (:parent #115)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #107))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #104) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #109))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #104)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #104) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #111))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #102))) :mode nil :granularity nil :parent #94) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #102) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #105) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #108)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #108) #("README" 0 6 (:parent #112))) #(".\n" 0 2 (:parent #108))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #103))) :mode nil :granularity nil :parent #94) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #103) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #106) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #109))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #104))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #107))) :mode section :granularity nil :parent #104) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #107) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #110) #("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 #113))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #110) #("As root configure the Guix profile\n" 0 35 (:parent #114))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #110)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #110) #("and run for example\n" 0 20 (:parent #116))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #110)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #110) #("If you want to run as root you may have to set\n" 0 47 (:parent #118))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #110) #("You also need to set\n" 0 21 (:parent #120))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #110) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #122))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #110) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #123))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #110) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #125))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #110) #("When you get errors like:\n" 0 26 (:parent #127))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #110)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #110) #("you may need to set\n" 0 20 (:parent #129))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #110)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #108))) :mode nil :granularity nil :parent #104) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #108) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #111) #("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 #114)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #114) #("webqtl" 0 6 (:parent #118))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #114) #("s" 0 1 (:parent #119))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #114)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #114) #("webqtl" 0 6 (:parent #121))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #114) #("plant" 0 5 (:parent #122))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #114))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #111) #("Download one database from\n" 0 27 (:parent #115))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #111) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #116)) #("\n" 0 1 (:parent #116))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #111) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #117))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #111) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #119))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #111)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #111) #("and\n" 0 4 (:parent #122))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #111) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #124))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #111)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #111) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #126))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #111) #("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 #127))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #111) #("Note for the plant database you can rename it to db" 0 51 (:parent #128)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #128) #("webqtl" 0 6 (:parent #132))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #128) #("s" 0 1 (:parent #133))) #(", or\nchange the settings in etc/default" 0 39 (:parent #128)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #128) #("settings.py" 0 11 (:parent #135))) #("to match your path.\n" 0 20 (:parent #128)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #105))) :mode nil :granularity nil :parent #94) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #105) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #108) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #111)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #111)) #("\n" 0 1 (:parent #111))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #108)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #106))) :mode nil :granularity nil :parent #94) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #106) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #109) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #112))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #109) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #("\n" 0 1 (:parent #113))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #107))) :mode nil :granularity nil :parent #94) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #107) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #110) #("See " 0 4 (:parent #113)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #113)) #(".\n" 0 2 (:parent #113))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #108))) :mode nil :granularity nil :parent #94) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #108) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #111) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #114)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #114))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #109))) :mode nil :granularity nil :parent #94) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #112))) :mode section :granularity nil :parent #109) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #112) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #115) #("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 #118)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #118) #("PATH" 0 4 (:parent #122))) #("and R" 0 5 (:parent #118)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #118) #("LIBS" 0 4 (:parent #124))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #118) #("SITE" 0 4 (:parent #125))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #118))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #115) #("On one system:\n" 0 15 (:parent #120))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #115)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #115) #("and perhaps a few more.\n" 0 24 (:parent #122))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #113)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #113) #("data" 0 4 (:parent #155))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #113)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #113) #("files" 0 5 (:parent #157))) #("/genotype'" 0 10 (:parent #113))) :mode nil :granularity nil :parent #109) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #113) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #116) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #119)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #119) #("data" 0 4 (:parent #123))) #(". 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 #119)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #119) #("settings.py" 0 11 (:parent #125))) #("(see above in\nthis document).\n" 0 30 (:parent #119))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #116) #("You can use the GENENETWORK" 0 27 (:parent #120)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #120) #("FILES" 0 5 (:parent #124))) #("switch to set the datadir, for example\n" 0 39 (:parent #120))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #116)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #114))) :mode nil :granularity nil :parent #109) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #114) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #117) #("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 #120))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #115))) :mode nil :granularity nil :parent #109) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #115) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #118) #("This error\n" 0 11 (:parent #121))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #118)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #118) #("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 #123))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #118) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #124)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #124) #("LIBS" 0 4 (:parent #128))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #124) #("SITE" 0 4 (:parent #129))) #(". 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 #124))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #116))) :mode nil :granularity nil :parent #109) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #116) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #119) #("The following error\n" 0 20 (:parent #122))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #119)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #119) #("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 #124))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #119)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #119) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #126))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #119)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #119) #("if that works run genenetwork after setting SQL" 0 47 (:parent #128)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #128) #("URI" 0 3 (:parent #132))) #("to something like\n" 0 18 (:parent #128))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #119))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #110))) :mode nil :granularity nil :parent #94) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #113))) :mode section :granularity nil :parent #110) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #113) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #116) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #119))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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"- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #120) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #123) #("Base install\n" 0 13 (:parent #126))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #123) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #127) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #130) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #133)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #127) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #131) #("Get Guix build going\n" 0 21 (:parent #134))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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"http://git.genenetwork.org/pjotrp/guix-bioinformatics" :application nil :search-option nil :begin 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #142)) #("\n" 0 1 (:parent #142)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" 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nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #127) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #132) #("Create a gn2 user and home with space\n" 0 38 (:parent #135)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #134) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #137))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #107) #("Guix bioinformatics" 0 19 (:parent #111))) #("and " 0 4 (:parent #107)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #107) #("GNU Guix" 0 8 (:parent #113))) #(".\n" 0 2 (:parent #107))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #103) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #108)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #108) #("GN2 Dependency Graph" 0 20 (:parent #112))) #(".\n" 0 2 (:parent #108))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #101))) :mode nil :granularity nil :parent #95) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #101) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #104) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #107)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #107)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #107))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #102))) :mode nil :granularity nil :parent #95) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #102) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #105) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #108)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #108) #("default" 0 7 (:parent #112)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #112) #("settings.py" 0 11 (:parent #116)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #108))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #105)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #105) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #110))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #105)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #105) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #112))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #103))) :mode nil :granularity nil :parent #95) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #103) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #106) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #109)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #109) #("README" 0 6 (:parent #113))) #(".\n" 0 2 (:parent #109))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #104))) :mode nil :granularity nil :parent #95) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #104) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #107) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #110))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #105))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #108))) :mode section :granularity nil :parent #105) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #108) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #111) #("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 #114))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #111) #("As root configure the Guix profile\n" 0 35 (:parent #115))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #111)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #111) #("and run for example\n" 0 20 (:parent #117))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #111)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #111) #("If you want to run as root you may have to set\n" 0 47 (:parent #119))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #111)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #111) #("You also need to set\n" 0 21 (:parent #121))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #111)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #111) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #123))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #111) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #124))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #111)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #111) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #126))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #111)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #111) #("When you get errors like:\n" 0 26 (:parent #128))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #111)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #111) #("you may need to set\n" 0 20 (:parent #130))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #111)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #109))) :mode nil :granularity nil :parent #105) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #109) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #112) #("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 #115)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #115) #("webqtl" 0 6 (:parent #119))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #115) #("s" 0 1 (:parent #120))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #115)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #115) #("webqtl" 0 6 (:parent #122))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #115) #("plant" 0 5 (:parent #123))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #115))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #112) #("Download one database from\n" 0 27 (:parent #116))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #112) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #117)) #("\n" 0 1 (:parent #117))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #112) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #118))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #112)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #112) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #120))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #112)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #112)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #112) #("and\n" 0 4 (:parent #123))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #112)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #112) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #125))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #112)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #112) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #127))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #112) #("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 #128))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #112) #("Note for the plant database you can rename it to db" 0 51 (:parent #129)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #129) #("webqtl" 0 6 (:parent #133))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #129) #("s" 0 1 (:parent #134))) #(", or\nchange the settings in etc/default" 0 39 (:parent #129)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #129) #("settings.py" 0 11 (:parent #136))) #("to match your path.\n" 0 20 (:parent #129)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #106))) :mode nil :granularity nil :parent #95) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #106) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #109) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #112)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #112)) #("\n" 0 1 (:parent #112))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #109)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #107))) :mode nil :granularity nil :parent #95) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #107) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #110) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #113))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #110) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #("\n" 0 1 (:parent #114))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #108))) :mode nil :granularity nil :parent #95) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #108) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #111) #("See " 0 4 (:parent #114)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #114)) #(".\n" 0 2 (:parent #114))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #109))) :mode nil :granularity nil :parent #95) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #109) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #112) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #115)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #115)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #115))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #110))) :mode nil :granularity nil :parent #95) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #113))) :mode section :granularity nil :parent #110) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #113) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #116) #("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 #119)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #119) #("PATH" 0 4 (:parent #123))) #("and R" 0 5 (:parent #119)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #119) #("LIBS" 0 4 (:parent #125))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #119) #("SITE" 0 4 (:parent #126))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #119))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #116)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #116) #("On one system:\n" 0 15 (:parent #121))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #116)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #116) #("and perhaps a few more.\n" 0 24 (:parent #123))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #114)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #114) #("data" 0 4 (:parent #156))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #114)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #114) #("files" 0 5 (:parent #158))) #("/genotype'" 0 10 (:parent #114))) :mode nil :granularity nil :parent #110) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #114) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #117) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #120)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #120) #("data" 0 4 (:parent #124))) #(". 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 #120)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #120) #("settings.py" 0 11 (:parent #126))) #("(see above in\nthis document).\n" 0 30 (:parent #120))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #117) #("You can use the GENENETWORK" 0 27 (:parent #121)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #121) #("FILES" 0 5 (:parent #125))) #("switch to set the datadir, for example\n" 0 39 (:parent #121))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #117)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #115))) :mode nil :granularity nil :parent #110) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #115) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #118) #("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 #121))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #116))) :mode nil :granularity nil :parent #110) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #116) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #119) #("This error\n" 0 11 (:parent #122))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #119)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #119) #("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 #124))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #119) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #125)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #125) #("LIBS" 0 4 (:parent #129))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #125) #("SITE" 0 4 (:parent #130))) #(". 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 #125))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #117))) :mode nil :granularity nil :parent #110) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #117) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #120) #("The following error\n" 0 20 (:parent #123))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #120)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #120) #("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 #125))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #120)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #120) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #127))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #120)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #120) #("if that works run genenetwork after setting SQL" 0 47 (:parent #129)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #129) #("URI" 0 3 (:parent #133))) #("to something like\n" 0 18 (:parent #129))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #120))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #111))) :mode nil :granularity nil :parent #95) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #114))) :mode section :granularity nil :parent #111) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #114) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #117) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #120))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #117) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #121) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #124) #("Base install\n" 0 13 (:parent #127))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #124) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #128) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #131) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #134)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #128) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #132) #("Get Guix build going\n" 0 21 (:parent #135))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #87))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #76) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #79) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #82)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #82)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #82))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #77))) :mode nil :granularity nil :parent #70) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #77) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #80) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #83)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #83) #("default" 0 7 (:parent #87)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #87) #("settings.py" 0 11 (:parent #91)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #83))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #80) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #85))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #80) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #87))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #78))) :mode nil :granularity nil :parent #70) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #78) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #81) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #84)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #84) #("README" 0 6 (:parent #88))) #(".\n" 0 2 (:parent #84))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #79) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #82) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #85))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #80))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 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:contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #86) #("and run for example\n" 0 20 (:parent #92))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #86)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #86) #("If you want to run as root you may have to set\n" 0 47 (:parent #94))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #86) #("You also need to set\n" 0 21 (:parent #96))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #86) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #98))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #86) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #99))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #86) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #101))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #86) #("When you get errors like:\n" 0 26 (:parent #103))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #86) #("you may need to set\n" 0 20 (:parent #105))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #86)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #84))) :mode nil :granularity nil :parent #80) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #84) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #87) #("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 #90)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #90) #("webqtl" 0 6 (:parent #94))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #90) #("s" 0 1 (:parent #95))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #90)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #90) #("webqtl" 0 6 (:parent #97))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #90) #("plant" 0 5 (:parent #98))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #90))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #87) #("Download one database from\n" 0 27 (:parent #91))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #87) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\n" 0 1 (:parent #92))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #87) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #93))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #87) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #95))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #87)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #87) #("and\n" 0 4 (:parent #98))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #87) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #100))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #87) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #102))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #87) #("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 #103))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #87) #("Note for the plant database you can rename it to db" 0 51 (:parent #104)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #104) #("webqtl" 0 6 (:parent #108))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #104) #("s" 0 1 (:parent #109))) #(", or\nchange the settings in etc/default" 0 39 (:parent #104)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #104) #("settings.py" 0 11 (:parent #111))) #("to match your path.\n" 0 20 (:parent #104)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #81) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #84) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #87)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #("\n" 0 1 (:parent #87))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #84)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #82))) :mode nil :granularity nil :parent #70) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #82) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #85) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #88))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #85) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #("\n" 0 1 (:parent #89))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #83) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #86) #("See " 0 4 (:parent #89)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #(".\n" 0 2 (:parent #89))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #84))) :mode nil :granularity nil :parent #70) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #84) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #87) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #90)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #90))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #85))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #88))) :mode section :granularity nil :parent #85) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #88) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #91) #("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 #94)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #94) #("PATH" 0 4 (:parent #98))) #("and R" 0 5 (:parent #94)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #94) #("LIBS" 0 4 (:parent #100))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #94) #("SITE" 0 4 (:parent #101))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #94))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #91) #("On one system:\n" 0 15 (:parent #96))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #91) #("and perhaps a few more.\n" 0 24 (:parent #98))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #89)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #89) #("data" 0 4 (:parent #131))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #89)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #89) #("files" 0 5 (:parent #133))) #("/genotype'" 0 10 (:parent #89))) :mode nil :granularity nil :parent #85) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #89) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #92) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #95)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #95) #("data" 0 4 (:parent #99))) #(". 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 #95)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #95) #("settings.py" 0 11 (:parent #101))) #("(see above in\nthis document).\n" 0 30 (:parent #95))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #92) #("You can use the GENENETWORK" 0 27 (:parent #96)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #96) #("FILES" 0 5 (:parent #100))) #("switch to set the datadir, for example\n" 0 39 (:parent #96))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #92)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #90))) :mode nil :granularity nil :parent #85) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #90) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #93) #("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 #96))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #91))) :mode nil :granularity nil :parent #85) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #91) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #94) #("This error\n" 0 11 (:parent #97))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #94)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #94) #("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 #99))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #94) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #100)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #100) #("LIBS" 0 4 (:parent #104))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #100) #("SITE" 0 4 (:parent #105))) #(". 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 #100))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #92))) :mode nil :granularity nil :parent #85) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #92) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #95) #("The following error\n" 0 20 (:parent #98))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #95)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #95) #("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 #100))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #95)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #95) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #102))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #95)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #95) #("if that works run genenetwork after setting SQL" 0 47 (:parent #104)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #104) #("URI" 0 3 (:parent #108))) #("to something like\n" 0 18 (:parent #104))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #95))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #86))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #89))) :mode section :granularity nil :parent #86) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #89) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #92) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #95))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #92) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #96) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #99) #("Base install\n" 0 13 (:parent #102))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #99) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #103) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #106) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #109)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #103) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #107) #("Get Guix build going\n" 0 21 (:parent #110))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #107) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #111) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #114) #("Build the correct version of Guix\n" 0 34 (:parent #117)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #111) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #115) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #118)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #118)) #("\n" 0 1 (:parent #118)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #111) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #116) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #119)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #103) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #108) #("Create a gn2 user and home with space\n" 0 38 (:parent #111)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 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"[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #109) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #116) #("add to systemd\n" 0 15 (:parent #119)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9933 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 9943 :end 9960 :contents-begin 9943 :contents-end 9960 :post-blank 0 :post-affiliated 9943 :mode nil :granularity nil :parent #117) #("update redis.cnf\n" 0 17 (:parent #120)))) (item (:bullet "- " :begin 9960 :end 9986 :contents-begin 9970 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9960 :tag nil :mode item :granularity nil :parent #113) (paragraph (:begin 9970 :end 9986 :contents-begin 9970 :contents-end 9986 :post-blank 0 :post-affiliated 9970 :mode nil :granularity nil :parent #118) #("update database\n" 0 16 (:parent #121)))))) (item (:bullet "+ " :begin 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #378) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #381))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10069 :tag nil :mode item :granularity nil :parent #382) (paragraph (:begin 10079 :end 10097 :contents-begin 10079 :contents-end 10097 :post-blank 0 :post-affiliated 10079 :mode nil :granularity nil :parent #386) #("system stop mysql\n" 0 18 (:parent #389)))) (item (:bullet "- " :begin 10097 :end 10124 :contents-begin 10107 :contents-end 10124 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- 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nil :parent #380) #("update nginx\n" 0 13 (:parent #383)))) (item (:bullet "+ " :begin 10248 :end 10302 :contents-begin 10256 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10248 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 10256 :end 10277 :contents-begin 10256 :contents-end 10277 :post-blank 0 :post-affiliated 10256 :mode nil :granularity nil :parent #381) #("install genenetwork3\n" 0 21 (:parent #384))) (plain-list (:type unordered :begin 10277 :end 10302 :contents-begin 10277 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10277 :mode nil :granularity nil :parent #381) (item (:bullet "- " :begin 10277 :end 10302 :contents-begin 10287 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10277 :tag nil :mode item :granularity nil :parent #385) (paragraph (:begin 10287 :end 10302 :contents-begin 10287 :contents-end 10302 :post-blank 0 :post-affiliated 10287 :mode nil :granularity nil :parent #388) #("add to systemd\n" 0 15 (:parent #391))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((section (:begin 121 :end 1309 :contents-begin 121 :contents-end 1308 :robust-begin 121 :robust-end 1306 :post-blank 1 :post-affiliated 121 :mode section :granularity nil :parent (headline (:raw-value "Table of Contents" :begin 43 :end 1309 :pre-blank 0 :contents-begin 121 :contents-end 1308 :robust-begin 123 :robust-end 1306 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #24))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #70) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #73))) #24 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #75))) :mode nil :granularity nil :parent #70) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #75) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #78) #("Large system deployments can get very " 0 38 (:parent #81)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #81) #("complex" 0 7 (:parent #85))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #81)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #81) #("Guix-notes" 0 10 (:parent #87))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #81))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #78) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #82) #("Guix bioinformatics" 0 19 (:parent #86))) #("and " 0 4 (:parent #82)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #82) #("GNU Guix" 0 8 (:parent #88))) #(".\n" 0 2 (:parent #82))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #78) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #83)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #83) #("GN2 Dependency Graph" 0 20 (:parent #87))) #(".\n" 0 2 (:parent #83))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #76))) :mode nil :granularity nil :parent #70) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #76) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #79) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #82)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #82)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #82))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #77))) :mode nil :granularity nil :parent #70) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #77) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #80) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #83)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #83) #("default" 0 7 (:parent #87)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #87) #("settings.py" 0 11 (:parent #91)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #83))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #80) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #85))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #80)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #80) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #87))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #78))) :mode nil :granularity nil :parent #70) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #78) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #81) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #84)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #84) #("README" 0 6 (:parent #88))) #(".\n" 0 2 (:parent #84))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #79))) :mode nil :granularity nil :parent #70) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #79) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #82) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #85))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #80))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #83))) :mode section :granularity nil :parent #80) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #83) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #86) #("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 #89))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #86) #("As root configure the Guix profile\n" 0 35 (:parent #90))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #86)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #86) #("and run for example\n" 0 20 (:parent #92))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #86)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #86) #("If you want to run as root you may have to set\n" 0 47 (:parent #94))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #86) #("You also need to set\n" 0 21 (:parent #96))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #86) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #98))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #86) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #99))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #86) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #101))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #86) #("When you get errors like:\n" 0 26 (:parent #103))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #86)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #86) #("you may need to set\n" 0 20 (:parent #105))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #86)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #84))) :mode nil :granularity nil :parent #80) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #84) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #87) #("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 #90)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #90) #("webqtl" 0 6 (:parent #94))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #90) #("s" 0 1 (:parent #95))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #90)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #90) #("webqtl" 0 6 (:parent #97))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #90) #("plant" 0 5 (:parent #98))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #90))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #87) #("Download one database from\n" 0 27 (:parent #91))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #87) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #92)) #("\n" 0 1 (:parent #92))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #87) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #93))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #87) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #95))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #87)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #87) #("and\n" 0 4 (:parent #98))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #87) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #100))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #87)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #87) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #102))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #87) #("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 #103))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #87) #("Note for the plant database you can rename it to db" 0 51 (:parent #104)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #104) #("webqtl" 0 6 (:parent #108))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #104) #("s" 0 1 (:parent #109))) #(", or\nchange the settings in etc/default" 0 39 (:parent #104)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #104) #("settings.py" 0 11 (:parent #111))) #("to match your path.\n" 0 20 (:parent #104)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #81))) :mode nil :granularity nil :parent #70) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #81) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #84) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #87)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #87)) #("\n" 0 1 (:parent #87))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #84)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #82))) :mode nil :granularity nil :parent #70) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #82) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #85) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #88))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #85) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #("\n" 0 1 (:parent #89))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #83))) :mode nil :granularity nil :parent #70) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #83) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #86) #("See " 0 4 (:parent #89)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #89)) #(".\n" 0 2 (:parent #89))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #84))) :mode nil :granularity nil :parent #70) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #84) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #87) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #90)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #90))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #85))) :mode nil :granularity nil :parent #70) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #88))) :mode section :granularity nil :parent #85) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #88) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #91) #("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 #94)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #94) #("PATH" 0 4 (:parent #98))) #("and R" 0 5 (:parent #94)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #94) #("LIBS" 0 4 (:parent #100))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #94) #("SITE" 0 4 (:parent #101))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #94))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #91) #("On one system:\n" 0 15 (:parent #96))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #91)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #91) #("and perhaps a few more.\n" 0 24 (:parent #98))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #89)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #89) #("data" 0 4 (:parent #131))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #89)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #89) #("files" 0 5 (:parent #133))) #("/genotype'" 0 10 (:parent #89))) :mode nil :granularity nil :parent #85) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #89) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #92) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #95)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #95) #("data" 0 4 (:parent #99))) #(". 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 #95)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #95) #("settings.py" 0 11 (:parent #101))) #("(see above in\nthis document).\n" 0 30 (:parent #95))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #92) #("You can use the GENENETWORK" 0 27 (:parent #96)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #96) #("FILES" 0 5 (:parent #100))) #("switch to set the datadir, for example\n" 0 39 (:parent #96))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #92)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #90))) :mode nil :granularity nil :parent #85) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #90) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #93) #("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 #96))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #91))) :mode nil :granularity nil :parent #85) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #91) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #94) #("This error\n" 0 11 (:parent #97))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #94)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #94) #("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 #99))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #94) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #100)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #100) #("LIBS" 0 4 (:parent #104))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #100) #("SITE" 0 4 (:parent #105))) #(". 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 #100))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #92))) :mode nil :granularity nil :parent #85) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #92) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #95) #("The following error\n" 0 20 (:parent #98))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #95)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #95) #("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 #100))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #95)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #95) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #102))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #95)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #95) #("if that works run genenetwork after setting SQL" 0 47 (:parent #104)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #104) #("URI" 0 3 (:parent #108))) #("to something like\n" 0 18 (:parent #104))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #95))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #86))) :mode nil :granularity nil :parent #70) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #89))) :mode section :granularity nil :parent #86) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #89) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #92) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #95))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #92) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil 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(9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #103) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #107) #("Get Guix build going\n" 0 21 (:parent #110))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #82)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #82) #("Guix-notes" 0 10 (:parent #88))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #82))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #79) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #83) #("Guix bioinformatics" 0 19 (:parent #87))) #("and " 0 4 (:parent #83)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #83) #("GNU Guix" 0 8 (:parent #89))) #(".\n" 0 2 (:parent #83))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #79) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #84)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #84) #("GN2 Dependency Graph" 0 20 (:parent #88))) #(".\n" 0 2 (:parent #84))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #77))) :mode nil :granularity nil :parent #71) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #77) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #80) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #83)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #83)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #83))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #78))) :mode nil :granularity nil :parent #71) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #78) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #81) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #84)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #84) #("default" 0 7 (:parent #88)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #88) #("settings.py" 0 11 (:parent #92)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #84))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #81)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #81) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #86))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #81)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #81) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #88))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #79))) :mode nil :granularity nil :parent #71) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #79) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #82) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #85)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #85) #("README" 0 6 (:parent #89))) #(".\n" 0 2 (:parent #85))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #80))) :mode nil :granularity nil :parent #71) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #80) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #83) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #86))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #81))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #84))) :mode section :granularity nil :parent #81) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #84) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #87) #("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 #90))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #87) #("As root configure the Guix profile\n" 0 35 (:parent #91))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #87)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #87) #("and run for example\n" 0 20 (:parent #93))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #87)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #87) #("If you want to run as root you may have to set\n" 0 47 (:parent #95))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #87)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #87) #("You also need to set\n" 0 21 (:parent #97))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #87)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #87) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #99))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #87) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #100))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #87)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #87) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #102))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #87)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #87) #("When you get errors like:\n" 0 26 (:parent #104))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #87)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #87) #("you may need to set\n" 0 20 (:parent #106))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #87)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #85))) :mode nil :granularity nil :parent #81) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #85) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #88) #("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 #91)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #91) #("webqtl" 0 6 (:parent #95))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #91) #("s" 0 1 (:parent #96))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #91)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #91) #("webqtl" 0 6 (:parent #98))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #91) #("plant" 0 5 (:parent #99))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #91))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #88) #("Download one database from\n" 0 27 (:parent #92))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #88) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #93)) #("\n" 0 1 (:parent #93))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #88) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #94))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #88)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #88) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #96))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #88)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #88)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #88) #("and\n" 0 4 (:parent #99))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #88)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #88) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #101))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #88)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #88) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #103))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #88) #("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 #104))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #88) #("Note for the plant database you can rename it to db" 0 51 (:parent #105)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #105) #("webqtl" 0 6 (:parent #109))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #105) #("s" 0 1 (:parent #110))) #(", or\nchange the settings in etc/default" 0 39 (:parent #105)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #105) #("settings.py" 0 11 (:parent #112))) #("to match your path.\n" 0 20 (:parent #105)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #82))) :mode nil :granularity nil :parent #71) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #82) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #85) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #88)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #88)) #("\n" 0 1 (:parent #88))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #85)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #83))) :mode nil :granularity nil :parent #71) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #83) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #86) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #89))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #86) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #("\n" 0 1 (:parent #90))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #84))) :mode nil :granularity nil :parent #71) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #84) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #87) #("See " 0 4 (:parent #90)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #90)) #(".\n" 0 2 (:parent #90))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #85))) :mode nil :granularity nil :parent #71) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #85) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #88) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #91)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #91)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #91))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #86))) :mode nil :granularity nil :parent #71) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #89))) :mode section :granularity nil :parent #86) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #89) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #92) #("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 #95)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #95) #("PATH" 0 4 (:parent #99))) #("and R" 0 5 (:parent #95)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #95) #("LIBS" 0 4 (:parent #101))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #95) #("SITE" 0 4 (:parent #102))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #95))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #92)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #92) #("On one system:\n" 0 15 (:parent #97))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #92)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #92) #("and perhaps a few more.\n" 0 24 (:parent #99))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #90)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #90) #("data" 0 4 (:parent #132))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #90)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #90) #("files" 0 5 (:parent #134))) #("/genotype'" 0 10 (:parent #90))) :mode nil :granularity nil :parent #86) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #90) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #93) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #96)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #96) #("data" 0 4 (:parent #100))) #(". 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 #96)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #96) #("settings.py" 0 11 (:parent #102))) #("(see above in\nthis document).\n" 0 30 (:parent #96))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #93) #("You can use the GENENETWORK" 0 27 (:parent #97)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #97) #("FILES" 0 5 (:parent #101))) #("switch to set the datadir, for example\n" 0 39 (:parent #97))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #93)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #91))) :mode nil :granularity nil :parent #86) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #91) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #94) #("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 #97))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #92))) :mode nil :granularity nil :parent #86) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #92) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #95) #("This error\n" 0 11 (:parent #98))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #95)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #95) #("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 #100))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #95) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #101)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #101) #("LIBS" 0 4 (:parent #105))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #101) #("SITE" 0 4 (:parent #106))) #(". 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 #101))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #93))) :mode nil :granularity nil :parent #86) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #93) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #96) #("The following error\n" 0 20 (:parent #99))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #96)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #96) #("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 #101))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #96)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #96) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #103))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #96)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #96) #("if that works run genenetwork after setting SQL" 0 47 (:parent #105)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #105) #("URI" 0 3 (:parent #109))) #("to something like\n" 0 18 (:parent #105))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #96))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #87))) :mode nil :granularity nil :parent #71) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #90))) :mode section :granularity nil :parent #87) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #90) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #93) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #96))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) 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:post-affiliated 9994 :mode nil :granularity nil :parent #111) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #114))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10069 :tag nil :mode item :granularity nil :parent #115) (paragraph (:begin 10079 :end 10097 :contents-begin 10079 :contents-end 10097 :post-blank 0 :post-affiliated 10079 :mode nil :granularity nil :parent #119) #("system stop mysql\n" 0 18 (:parent #122)))) (item (:bullet "- " :begin 10097 :end 10124 :contents-begin 10107 :contents-end 10124 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- 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Follow the instructions on\n" 0 117 (:parent #58)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #58)) #("to download pre-built binaries. 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You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #59))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #56) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #61))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #56) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #63))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #54))) :mode nil :granularity nil :parent #46) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #54) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #57) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #60)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #60) #("README" 0 6 (:parent #64))) #(".\n" 0 2 (:parent #60))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #55) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #58) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #61))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #56))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #59))) :mode section :granularity nil :parent #56) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #59) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #62) #("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 #65))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #62) #("As root configure the Guix profile\n" 0 35 (:parent #66))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #62)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #62) #("and run for example\n" 0 20 (:parent #68))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #62)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #62) #("If you want to run as root you may have to set\n" 0 47 (:parent #70))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #62) #("You also need to set\n" 0 21 (:parent #72))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #62) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #74))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #62) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #75))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #62) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #77))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #62) #("When you get errors like:\n" 0 26 (:parent #79))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #62) #("you may need to set\n" 0 20 (:parent #81))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #62)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #60))) :mode nil :granularity nil :parent #56) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #60) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #63) #("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 #66)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #66) #("webqtl" 0 6 (:parent #70))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #66) #("s" 0 1 (:parent #71))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #66)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #66) #("webqtl" 0 6 (:parent #73))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #66) #("plant" 0 5 (:parent #74))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #66))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #63) #("Download one database from\n" 0 27 (:parent #67))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #63) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #("\n" 0 1 (:parent #68))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #63) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #69))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #63) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #71))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #63)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #63) #("and\n" 0 4 (:parent #74))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #63) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #76))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #63) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #78))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #63) #("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 #79))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #63) #("Note for the plant database you can rename it to db" 0 51 (:parent #80)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #80) #("webqtl" 0 6 (:parent #84))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #80) #("s" 0 1 (:parent #85))) #(", or\nchange the settings in etc/default" 0 39 (:parent #80)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #80) #("settings.py" 0 11 (:parent #87))) #("to match your path.\n" 0 20 (:parent #80)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #57) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #60) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #63)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #("\n" 0 1 (:parent #63))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #60)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #58))) :mode nil :granularity nil :parent #46) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #58) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #61) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #64))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #61) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #("\n" 0 1 (:parent #65))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #59) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #62) #("See " 0 4 (:parent #65)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #(".\n" 0 2 (:parent #65))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #60))) :mode nil :granularity nil :parent #46) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #60) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #63) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #66)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #66)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #66))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #61))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #64))) :mode section :granularity nil :parent #61) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #64) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #67) #("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 #70)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #70) #("PATH" 0 4 (:parent #74))) #("and R" 0 5 (:parent #70)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #70) #("LIBS" 0 4 (:parent #76))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #70) #("SITE" 0 4 (:parent #77))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #70))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #67) #("On one system:\n" 0 15 (:parent #72))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #67) #("and perhaps a few more.\n" 0 24 (:parent #74))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #65)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #65) #("data" 0 4 (:parent #107))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #65)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #65) #("files" 0 5 (:parent #109))) #("/genotype'" 0 10 (:parent #65))) :mode nil :granularity nil :parent #61) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #65) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #68) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #71)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #71) #("data" 0 4 (:parent #75))) #(". 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 #71)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #71) #("settings.py" 0 11 (:parent #77))) #("(see above in\nthis document).\n" 0 30 (:parent #71))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #68) #("You can use the GENENETWORK" 0 27 (:parent #72)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #72) #("FILES" 0 5 (:parent #76))) #("switch to set the datadir, for example\n" 0 39 (:parent #72))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #68)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #66))) :mode nil :granularity nil :parent #61) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #66) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #69) #("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 #72))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #67))) :mode nil :granularity nil :parent #61) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #67) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #70) #("This error\n" 0 11 (:parent #73))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #70)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #70) #("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 #75))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #70) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #76)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #76) #("LIBS" 0 4 (:parent #80))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #76) #("SITE" 0 4 (:parent #81))) #(". 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 #76))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #68))) :mode nil :granularity nil :parent #61) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #68) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #71) #("The following error\n" 0 20 (:parent #74))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #71)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #71) #("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 #76))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #71)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #71) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #78))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #71)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #71) #("if that works run genenetwork after setting SQL" 0 47 (:parent #80)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #80) #("URI" 0 3 (:parent #84))) #("to something like\n" 0 18 (:parent #80))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #71))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #62))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #65))) :mode section :granularity nil :parent #62) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #65) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #68) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #71))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #68) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #72) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #75) #("Base install\n" 0 13 (:parent #78))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #75) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #82) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #85)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #83) #("Get Guix build going\n" 0 21 (:parent #86))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #83) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #90) #("Build the correct version of Guix\n" 0 34 (:parent #93)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #91) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #94)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #94)) #("\n" 0 1 (:parent #94)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #92) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #95)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #84) #("Create a gn2 user and home with space\n" 0 38 (:parent #87)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #85) #("Install redis\n" 0 14 (:parent #88))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #85) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" 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:contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #343) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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(10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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:post-affiliated 9994 :mode nil :granularity nil :parent #378) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #381))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 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nil :parent #380) #("update nginx\n" 0 13 (:parent #383)))) (item (:bullet "+ " :begin 10248 :end 10302 :contents-begin 10256 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10248 :tag nil :mode item :granularity nil :parent #371) (paragraph (:begin 10256 :end 10277 :contents-begin 10256 :contents-end 10277 :post-blank 0 :post-affiliated 10256 :mode nil :granularity nil :parent #381) #("install genenetwork3\n" 0 21 (:parent #384))) (plain-list (:type unordered :begin 10277 :end 10302 :contents-begin 10277 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 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nil :mode item :granularity nil :parent #385) (paragraph (:begin 10287 :end 10302 :contents-begin 10287 :contents-end 10302 :post-blank 0 :post-affiliated 10287 :mode nil :granularity nil :parent #388) #("add to systemd\n" 0 15 (:parent #391))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) #f(compiled-function (element) #)((headline (:raw-value "Table of Contents" :begin 43 :end 1309 :pre-blank 0 :contents-begin 121 :contents-end 1308 :robust-begin 123 :robust-end 1306 :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 :title (#("Table of Contents" 0 17 (:parent #0))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) (section (:begin 1 :end 43 :contents-begin 1 :contents-end 42 :robust-begin 1 :robust-end 40 :post-blank 1 :post-affiliated 1 :mode first-section :granularity nil :parent #46) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #49))) #0 (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #51))) :mode nil :granularity nil :parent #46) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #51) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #54) #("Large system deployments can get very " 0 38 (:parent #57)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #57) #("complex" 0 7 (:parent #61))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #57)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #57) #("Guix-notes" 0 10 (:parent #63))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #57))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #54) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #58) #("Guix bioinformatics" 0 19 (:parent #62))) #("and " 0 4 (:parent #58)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #58) #("GNU Guix" 0 8 (:parent #64))) #(".\n" 0 2 (:parent #58))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #54) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #59)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #59) #("GN2 Dependency Graph" 0 20 (:parent #63))) #(".\n" 0 2 (:parent #59))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #52))) :mode nil :granularity nil :parent #46) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #52) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #55) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #58)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #58)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #58))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #53))) :mode nil :granularity nil :parent #46) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #53) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #56) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #59)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #59) #("default" 0 7 (:parent #63)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #63) #("settings.py" 0 11 (:parent #67)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #59))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #56) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #61))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #56)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #56) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #63))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #54))) :mode nil :granularity nil :parent #46) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #54) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #57) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #60)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #60) #("README" 0 6 (:parent #64))) #(".\n" 0 2 (:parent #60))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #55))) :mode nil :granularity nil :parent #46) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #55) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #58) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #61))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #56))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #59))) :mode section :granularity nil :parent #56) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #59) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #62) #("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 #65))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #62) #("As root configure the Guix profile\n" 0 35 (:parent #66))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #62)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #62) #("and run for example\n" 0 20 (:parent #68))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #62)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #62) #("If you want to run as root you may have to set\n" 0 47 (:parent #70))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #62) #("You also need to set\n" 0 21 (:parent #72))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #62) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #74))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #62) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #75))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #62) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #77))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #62) #("When you get errors like:\n" 0 26 (:parent #79))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #62)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #62) #("you may need to set\n" 0 20 (:parent #81))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #62)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #60))) :mode nil :granularity nil :parent #56) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #60) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #63) #("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 #66)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #66) #("webqtl" 0 6 (:parent #70))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #66) #("s" 0 1 (:parent #71))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #66)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #66) #("webqtl" 0 6 (:parent #73))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #66) #("plant" 0 5 (:parent #74))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #66))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #63) #("Download one database from\n" 0 27 (:parent #67))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #63) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #68)) #("\n" 0 1 (:parent #68))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #63) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #69))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #63) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #71))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #63)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #63) #("and\n" 0 4 (:parent #74))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #63) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #76))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #63)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #63) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #78))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #63) #("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 #79))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #63) #("Note for the plant database you can rename it to db" 0 51 (:parent #80)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #80) #("webqtl" 0 6 (:parent #84))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #80) #("s" 0 1 (:parent #85))) #(", or\nchange the settings in etc/default" 0 39 (:parent #80)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #80) #("settings.py" 0 11 (:parent #87))) #("to match your path.\n" 0 20 (:parent #80)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #57))) :mode nil :granularity nil :parent #46) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #57) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #60) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #63)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #63)) #("\n" 0 1 (:parent #63))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #60)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #58))) :mode nil :granularity nil :parent #46) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #58) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #61) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #64))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #61) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #("\n" 0 1 (:parent #65))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #59))) :mode nil :granularity nil :parent #46) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #59) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #62) #("See " 0 4 (:parent #65)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #65)) #(".\n" 0 2 (:parent #65))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #60))) :mode nil :granularity nil :parent #46) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #60) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #63) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #66)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #66)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #66))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #61))) :mode nil :granularity nil :parent #46) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #64))) :mode section :granularity nil :parent #61) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #64) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #67) #("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 #70)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #70) #("PATH" 0 4 (:parent #74))) #("and R" 0 5 (:parent #70)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #70) #("LIBS" 0 4 (:parent #76))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #70) #("SITE" 0 4 (:parent #77))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #70))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #67) #("On one system:\n" 0 15 (:parent #72))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #67)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #67) #("and perhaps a few more.\n" 0 24 (:parent #74))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #65)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #65) #("data" 0 4 (:parent #107))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #65)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #65) #("files" 0 5 (:parent #109))) #("/genotype'" 0 10 (:parent #65))) :mode nil :granularity nil :parent #61) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #65) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #68) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #71)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #71) #("data" 0 4 (:parent #75))) #(". 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 #71)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #71) #("settings.py" 0 11 (:parent #77))) #("(see above in\nthis document).\n" 0 30 (:parent #71))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #68) #("You can use the GENENETWORK" 0 27 (:parent #72)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #72) #("FILES" 0 5 (:parent #76))) #("switch to set the datadir, for example\n" 0 39 (:parent #72))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #68)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #66))) :mode nil :granularity nil :parent #61) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #66) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #69) #("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 #72))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #67))) :mode nil :granularity nil :parent #61) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #67) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #70) #("This error\n" 0 11 (:parent #73))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #70)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #70) #("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 #75))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #70) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #76)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #76) #("LIBS" 0 4 (:parent #80))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #76) #("SITE" 0 4 (:parent #81))) #(". 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 #76))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #68))) :mode nil :granularity nil :parent #61) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #68) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #71) #("The following error\n" 0 20 (:parent #74))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #71)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #71) #("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 #76))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #71)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #71) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #78))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #71)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #71) #("if that works run genenetwork after setting SQL" 0 47 (:parent #80)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #80) #("URI" 0 3 (:parent #84))) #("to something like\n" 0 18 (:parent #80))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #71))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #62))) :mode nil :granularity nil :parent #46) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #65))) :mode section :granularity nil :parent #62) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #65) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #68) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #71))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9482 :mode nil :granularity nil :parent #68) (item (:bullet "- " :begin 9482 :end 10302 :contents-begin 9488 :contents-end 10302 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #72) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #75) #("Base install\n" 0 13 (:parent #78))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #75) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #82) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #85)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #83) #("Get Guix build going\n" 0 21 (:parent #86))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9591 :mode nil :granularity nil :parent #83) (item (:bullet "- " :begin 9591 :end 9635 :contents-begin 9601 :contents-end 9635 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #90) #("Build the correct version of Guix\n" 0 34 (:parent #93)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9635 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9645 :end 9762 :contents-begin 9645 :contents-end 9762 :post-blank 0 :post-affiliated 9645 :mode nil :granularity nil :parent #91) #("Check out the correct gn-stable version of guix-bioinformatics " 0 63 (:parent #94)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #94)) #("\n" 0 1 (:parent #94)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #87) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #92) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #95)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #84) #("Create a gn2 user and home with space\n" 0 38 (:parent #87)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9886 :tag nil :mode item :granularity nil :parent #79) (paragraph (:begin 9894 :end 9908 :contents-begin 9894 :contents-end 9908 :post-blank 0 :post-affiliated 9894 :mode nil :granularity nil :parent #85) #("Install redis\n" 0 14 (:parent #88))) (plain-list (:type unordered :begin 9908 :end 9986 :contents-begin 9908 :contents-end 9986 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9908 :mode nil :granularity nil :parent #85) (item (:bullet "- " :begin 9908 :end 9933 :contents-begin 9918 :contents-end 9933 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #92) #("add to systemd\n" 0 15 (:parent #95)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9933 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 9943 :end 9960 :contents-begin 9943 :contents-end 9960 :post-blank 0 :post-affiliated 9943 :mode nil :granularity nil :parent #93) #("update redis.cnf\n" 0 17 (:parent #96)))) (item (:bullet "- " :begin 9960 :end 9986 :contents-begin 9970 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9960 :tag nil :mode item :granularity nil :parent #89) (paragraph (:begin 9970 :end 9986 :contents-begin 9970 :contents-end 9986 :post-blank 0 :post-affiliated 9970 :mode nil :granularity nil :parent #94) #("update database\n" 0 16 (:parent #97)))))) (item (:bullet "+ " :begin 9986 :end 10211 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9994 :mode nil :granularity nil :parent #86) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #89))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 :mode nil 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:mode nil :granularity nil :parent #29) (link (:type "custom-id" :path "deploying-gn2-official" :format bracket :raw-link "#deploying-gn2-official" :application nil :search-option nil :begin 1256 :end 1307 :contents-begin 1283 :contents-end 1305 :post-blank 0 :parent #32) #("Deploying GN2 official" 0 22 (:parent #35))) #("\n" 0 1 (:parent #32))))))))) (headline (:raw-value "Introduction" :begin 1309 :end 2197 :pre-blank 1 :contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #3))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #3) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #6) #("Large system deployments can get very " 0 38 (:parent #9)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #9) #("complex" 0 7 (:parent #13))) #(". 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 (: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 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #9) #("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 (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #6) #("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 #10)) (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 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #10) #("Guix bioinformatics" 0 19 (:parent #14))) #("and " 0 4 (:parent #10)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #10) #("GNU Guix" 0 8 (:parent #16))) #(".\n" 0 2 (:parent #10))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #6) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #11)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #11) #("GN2 Dependency Graph" 0 20 (:parent #15))) #(".\n" 0 2 (:parent #11))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #4))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #4) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #7) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #10)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #10)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #10))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #5))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #5) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #8) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #11)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #11) #("default" 0 7 (:parent #15)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #15) #("settings.py" 0 11 (:parent #19)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #11))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #8)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #8) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #13))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #8)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #8) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #15))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #6))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #6) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #9) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #12)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #12) #("README" 0 6 (:parent #16))) #(".\n" 0 2 (:parent #12))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #7))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #7) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #10) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #13))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #8))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #11))) :mode section :granularity nil :parent #8) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #11) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #14) #("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 #17))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #14) #("As root configure the Guix profile\n" 0 35 (:parent #18))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #14) #("and run for example\n" 0 20 (:parent #20))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #14)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #14) #("If you want to run as root you may have to set\n" 0 47 (:parent #22))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #14) #("You also need to set\n" 0 21 (:parent #24))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #14) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #26))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #14) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #27))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #14) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #29))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #14) #("When you get errors like:\n" 0 26 (:parent #31))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #14)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #14) #("you may need to set\n" 0 20 (:parent #33))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #14)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #12))) :mode nil :granularity nil :parent #8) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #12) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #15) #("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 #18)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #18) #("webqtl" 0 6 (:parent #22))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #18) #("s" 0 1 (:parent #23))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #18)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #18) #("webqtl" 0 6 (:parent #25))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #18) #("plant" 0 5 (:parent #26))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #18))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #15) #("Download one database from\n" 0 27 (:parent #19))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #15) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #20)) #("\n" 0 1 (:parent #20))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #15) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #21))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #15) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #23))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #15)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #15) #("and\n" 0 4 (:parent #26))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #15) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #28))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #15)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #15) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #30))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #15) #("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 #31))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #15) #("Note for the plant database you can rename it to db" 0 51 (:parent #32)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #32) #("webqtl" 0 6 (:parent #36))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #32) #("s" 0 1 (:parent #37))) #(", or\nchange the settings in etc/default" 0 39 (:parent #32)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #32) #("settings.py" 0 11 (:parent #39))) #("to match your path.\n" 0 20 (:parent #32)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #9))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #9) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #12) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #15)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #15)) #("\n" 0 1 (:parent #15))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #12)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #10))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #10) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #13) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #16))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #13) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #("\n" 0 1 (:parent #17))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #11))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #11) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #14) #("See " 0 4 (:parent #17)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #(".\n" 0 2 (:parent #17))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #12))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #12) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #15) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #18)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #18)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #18))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #13))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #16))) :mode section :granularity nil :parent #13) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #16) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #19) #("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 #22)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #22) #("PATH" 0 4 (:parent #26))) #("and R" 0 5 (:parent #22)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #22) #("LIBS" 0 4 (:parent #28))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #22) #("SITE" 0 4 (:parent #29))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #22))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #19)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #19) #("On one system:\n" 0 15 (:parent #24))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #19)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #19) #("and perhaps a few more.\n" 0 24 (:parent #26))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #17)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #17) #("data" 0 4 (:parent #59))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #17)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #17) #("files" 0 5 (:parent #61))) #("/genotype'" 0 10 (:parent #17))) :mode nil :granularity nil :parent #13) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #17) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #20) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #23)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #23) #("data" 0 4 (:parent #27))) #(". 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 #23)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #23) #("settings.py" 0 11 (:parent #29))) #("(see above in\nthis document).\n" 0 30 (:parent #23))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #20) #("You can use the GENENETWORK" 0 27 (:parent #24)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #24) #("FILES" 0 5 (:parent #28))) #("switch to set the datadir, for example\n" 0 39 (:parent #24))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #20)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #18))) :mode nil :granularity nil :parent #13) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #18) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #21) #("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 #24))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #19))) :mode nil :granularity nil :parent #13) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #19) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #22) #("This error\n" 0 11 (:parent #25))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #22)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #22) #("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 #27))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #22) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #28)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #28) #("LIBS" 0 4 (:parent #32))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #28) #("SITE" 0 4 (:parent #33))) #(". 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 #28))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #20))) :mode nil :granularity nil :parent #13) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #20) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #23) #("The following error\n" 0 20 (:parent #26))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #23)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #23) #("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 #28))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #23)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #23) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #30))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #23)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #23) #("if that works run genenetwork after setting SQL" 0 47 (:parent #32)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #32) #("URI" 0 3 (:parent #36))) #("to something like\n" 0 18 (:parent #32))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #23))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #14))) :mode nil :granularity nil :parent (org-data (:begin 1 :contents-begin 1 :contents-end 10302 :end 10302 :robust-begin 3 :robust-end 10300 :post-blank 0 :post-affiliated 1 :path nil :mode org-data :CATEGORY nil :granularity nil) . #0)) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #17))) :mode section :granularity nil :parent #14) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #17) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #20) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #23))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- 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(9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #24) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #27) #("Base install\n" 0 13 (:parent #30))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #27) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #31) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #34) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #37)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9562 :tag nil :mode item :granularity nil :parent #31) (paragraph (:begin 9570 :end 9591 :contents-begin 9570 :contents-end 9591 :post-blank 0 :post-affiliated 9570 :mode nil :granularity nil :parent #35) #("Get Guix build going\n" 0 21 (:parent #38))) (plain-list (:type unordered :begin 9591 :end 9840 :contents-begin 9591 :contents-end 9840 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 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"[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9591 :tag nil :mode item :granularity nil :parent #39) (paragraph (:begin 9601 :end 9635 :contents-begin 9601 :contents-end 9635 :post-blank 0 :post-affiliated 9601 :mode nil :granularity nil :parent #42) #("Build the correct version of Guix\n" 0 34 (:parent #45)))) (item (:bullet "- " :begin 9635 :end 9762 :contents-begin 9645 :contents-end 9762 :checkbox off :counter nil :structure 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version of guix-bioinformatics " 0 63 (:parent #46)) (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 9708 :end 9761 :contents-begin nil :contents-end nil :post-blank 0 :parent #46)) #("\n" 0 1 (:parent #46)))) (item (:bullet "- " :begin 9762 :end 9840 :contents-begin 9772 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9762 :tag nil :mode item :granularity nil :parent #39) (paragraph (:begin 9772 :end 9840 :contents-begin 9772 :contents-end 9840 :post-blank 0 :post-affiliated 9772 :mode nil :granularity nil :parent #44) #("guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable\n" 0 68 (:parent #47)))))) (item (:bullet "+ " :begin 9840 :end 9886 :contents-begin 9848 :contents-end 9886 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9840 :tag nil :mode item :granularity nil :parent #31) (paragraph (:begin 9848 :end 9886 :contents-begin 9848 :contents-end 9886 :post-blank 0 :post-affiliated 9848 :mode nil :granularity nil :parent #36) #("Create a gn2 user and home with space\n" 0 38 (:parent #39)))) (item (:bullet "+ " :begin 9886 :end 9986 :contents-begin 9894 :contents-end 9986 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " 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(9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9933 :tag nil :mode item :granularity nil :parent #41) (paragraph (:begin 9943 :end 9960 :contents-begin 9943 :contents-end 9960 :post-blank 0 :post-affiliated 9943 :mode nil :granularity nil :parent #45) #("update redis.cnf\n" 0 17 (:parent #48)))) (item (:bullet "- " :begin 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:post-affiliated 9970 :mode nil :granularity nil :parent #46) #("update database\n" 0 16 (:parent #49)))))) (item (:bullet "+ " :begin 9986 :end 10211 :contents-begin 9994 :contents-end 10211 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9986 :tag 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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 #11)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #11) #("Guix-notes" 0 10 (:parent #17))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #11))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #8) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #12) #("Guix bioinformatics" 0 19 (:parent #16))) #("and " 0 4 (:parent #12)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #12) #("GNU Guix" 0 8 (:parent #18))) #(".\n" 0 2 (:parent #12))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #8) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #13)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #13) #("GN2 Dependency Graph" 0 20 (:parent #17))) #(".\n" 0 2 (:parent #13))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #6))) :mode nil :granularity nil :parent #0) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #6) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #9) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #12)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #12)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #12))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #7))) :mode nil :granularity nil :parent #0) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #7) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #10) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #13)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #13) #("default" 0 7 (:parent #17)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #17) #("settings.py" 0 11 (:parent #21)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #13))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #10)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #10) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #15))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #10)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #10) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #17))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #8))) :mode nil :granularity nil :parent #0) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #8) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #11) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #14)) (link (:type "https" :path "//github.com/genenetwork/gn-proxy" :format bracket :raw-link "https://github.com/genenetwork/gn-proxy" :application nil :search-option nil :begin 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #14) #("README" 0 6 (:parent #18))) #(".\n" 0 2 (:parent #14))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #9))) :mode nil :granularity nil :parent #0) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #9) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #12) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #15))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #10))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #13))) :mode section :granularity nil :parent #10) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #13) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #16) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #19))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #16) #("As root configure the Guix profile\n" 0 35 (:parent #20))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #16)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #16) #("and run for example\n" 0 20 (:parent #22))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #16)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #16) #("If you want to run as root you may have to set\n" 0 47 (:parent #24))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #16)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #16) #("You also need to set\n" 0 21 (:parent #26))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #16)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #16) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #28))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #16) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #29))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #16)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #16) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #31))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #16)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #16) #("When you get errors like:\n" 0 26 (:parent #33))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #16)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #16) #("you may need to set\n" 0 20 (:parent #35))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #16)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #14))) :mode nil :granularity nil :parent #10) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #14) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #17) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #20)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #20) #("webqtl" 0 6 (:parent #24))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #20) #("s" 0 1 (:parent #25))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #20)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #20) #("webqtl" 0 6 (:parent #27))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #20) #("plant" 0 5 (:parent #28))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #20))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #17) #("Download one database from\n" 0 27 (:parent #21))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #17) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk" :application nil :search-option nil :begin 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #22)) #("\n" 0 1 (:parent #22))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #17) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #23))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #17)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #17) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #25))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #17)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #17)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #17) #("and\n" 0 4 (:parent #28))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #17)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #17) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #30))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #17)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #17) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #32))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #17) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #33))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #17) #("Note for the plant database you can rename it to db" 0 51 (:parent #34)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #34) #("webqtl" 0 6 (:parent #38))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #34) #("s" 0 1 (:parent #39))) #(", or\nchange the settings in etc/default" 0 39 (:parent #34)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #34) #("settings.py" 0 11 (:parent #41))) #("to match your path.\n" 0 20 (:parent #34)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #11))) :mode nil :granularity nil :parent #0) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #11) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #14) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #17)) (link (:type "http" :path "//ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :format plain :raw-link "http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL" :application nil :search-option nil :begin 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #17)) #("\n" 0 1 (:parent #17))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #14)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #12))) :mode nil :granularity nil :parent #0) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #12) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #15) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #18))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #15) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #("\n" 0 1 (:parent #19))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #13))) :mode nil :granularity nil :parent #0) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #13) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #16) #("See " 0 4 (:parent #19)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #19)) #(".\n" 0 2 (:parent #19))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #14))) :mode nil :granularity nil :parent #0) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #14) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #17) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #20)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #20)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #20))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #15))) :mode nil :granularity nil :parent #0) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #18))) :mode section :granularity nil :parent #15) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #18) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #21) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #24)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #24) #("PATH" 0 4 (:parent #28))) #("and R" 0 5 (:parent #24)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #24) #("LIBS" 0 4 (:parent #30))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #24) #("SITE" 0 4 (:parent #31))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #24))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #21)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #21) #("On one system:\n" 0 15 (:parent #26))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #21)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #21) #("and perhaps a few more.\n" 0 24 (:parent #28))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #19)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #19) #("data" 0 4 (:parent #61))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #19)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #19) #("files" 0 5 (:parent #63))) #("/genotype'" 0 10 (:parent #19))) :mode nil :granularity nil :parent #15) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #19) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #22) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #25)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #25) #("data" 0 4 (:parent #29))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #25)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #25) #("settings.py" 0 11 (:parent #31))) #("(see above in\nthis document).\n" 0 30 (:parent #25))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #22) #("You can use the GENENETWORK" 0 27 (:parent #26)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #26) #("FILES" 0 5 (:parent #30))) #("switch to set the datadir, for example\n" 0 39 (:parent #26))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #22)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #20))) :mode nil :granularity nil :parent #15) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #20) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #23) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #26))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #21))) :mode nil :granularity nil :parent #15) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #21) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #24) #("This error\n" 0 11 (:parent #27))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #24)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #24) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #29))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #24) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #30)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #30) #("LIBS" 0 4 (:parent #34))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #30) #("SITE" 0 4 (:parent #35))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #30))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #22))) :mode nil :granularity nil :parent #15) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #22) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #25) #("The following error\n" 0 20 (:parent #28))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #25)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #25) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #30))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #25)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #25) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #32))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #25)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #25) #("if that works run genenetwork after setting SQL" 0 47 (:parent #34)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #34) #("URI" 0 3 (:parent #38))) #("to something like\n" 0 18 (:parent #34))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #25))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #16))) :mode nil :granularity nil :parent #0) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #19))) :mode section :granularity nil :parent #16) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #19) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #22) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #25))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 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(10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9501 :tag nil :mode item :granularity nil :parent #33) (paragraph (:begin 9509 :end 9562 :contents-begin 9509 :contents-end 9562 :post-blank 0 :post-affiliated 9509 :mode nil :granularity nil :parent #36) #("First install a Debian server with GNU Guix on board\n" 0 53 (:parent #39)))) (item (:bullet "+ " :begin 9562 :end 9840 :contents-begin 9570 :contents-end 9840 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 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nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9908 :tag nil :mode item :granularity nil :parent #43) (paragraph (:begin 9918 :end 9933 :contents-begin 9918 :contents-end 9933 :post-blank 0 :post-affiliated 9918 :mode nil :granularity nil :parent #46) #("add to systemd\n" 0 15 (:parent #49)))) (item (:bullet "- " :begin 9933 :end 9960 :contents-begin 9943 :contents-end 9960 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 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9994 :mode nil :granularity nil :parent #40) #("Install mariadb (currently debian mariadb-server)\n" 0 50 (:parent #43))) (plain-list (:type unordered :begin 10044 :end 10211 :contents-begin 10044 :contents-end 10211 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 10044 :mode nil 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:contents-begin 1325 :contents-end 2196 :robust-begin 1327 :robust-end 2194 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1309 :title (#("Introduction" 0 12 (:parent #343))) :mode nil :granularity nil :parent #338) (section (:begin 1325 :end 2197 :contents-begin 1325 :contents-end 2196 :robust-begin 1325 :robust-end 2194 :post-blank 1 :post-affiliated 1325 :mode section :granularity nil :parent #343) (paragraph (:begin 1325 :end 1711 :contents-begin 1325 :contents-end 1710 :post-blank 1 :post-affiliated 1325 :mode planning :granularity nil :parent #346) #("Large system deployments can get very " 0 38 (:parent #349)) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg " :format bracket :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg " :application nil :search-option nil :begin 1363 :end 1424 :contents-begin 1415 :contents-end 1422 :post-blank 0 :parent #349) #("complex" 0 7 (:parent #353))) #(". In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1554 :end 1628 :contents-begin 1616 :contents-end 1626 :post-blank 0 :parent #349) #("Guix-notes" 0 10 (:parent #355))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #349))) (paragraph (:begin 1711 :end 2061 :contents-begin 1711 :contents-end 2060 :post-blank 1 :post-affiliated 1711 :mode nil :granularity nil :parent #346) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1929 :end 2005 :contents-begin 1983 :contents-end 2002 :post-blank 1 :parent #350) #("Guix bioinformatics" 0 19 (:parent #354))) #("and " 0 4 (:parent #350)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2009 :end 2058 :contents-begin 2048 :contents-end 2056 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2061 :end 2196 :contents-begin 2061 :contents-end 2196 :post-blank 0 :post-affiliated 2061 :mode nil :granularity nil :parent #346) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #351)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2147 :end 2194 :contents-begin 2172 :contents-end 2192 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2197 :end 2446 :pre-blank 1 :contents-begin 2208 :contents-end 2445 :robust-begin 2210 :robust-end 2443 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2197 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2208 :end 2446 :contents-begin 2208 :contents-end 2445 :robust-begin 2208 :robust-end 2443 :post-blank 1 :post-affiliated 2208 :mode section :granularity nil :parent #344) (paragraph (:begin 2208 :end 2445 :contents-begin 2208 :contents-end 2445 :post-blank 0 :post-affiliated 2208 :mode planning :granularity nil :parent #347) #("Make sure to install GNU Guix using the binary download instructions\non the main website. Follow the instructions on\n" 0 117 (:parent #350)) (link (:type "fuzzy" :path "GUIX-Reproducible-from-source.org" :format bracket :raw-link "GUIX-Reproducible-from-source.org" :application nil :search-option nil :begin 2325 :end 2363 :contents-begin nil :contents-end nil :post-blank 1 :parent #350)) #("to download pre-built binaries. Note\nthe download amounts to several GBs of data.\n" 0 82 (:parent #350))))) (headline (:raw-value "Running GN2" :begin 2446 :end 2927 :pre-blank 1 :contents-begin 2461 :contents-end 2926 :robust-begin 2463 :robust-end 2924 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2446 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 2461 :end 2927 :contents-begin 2461 :contents-end 2926 :robust-begin 2461 :robust-end 2924 :post-blank 1 :post-affiliated 2461 :mode section :granularity nil :parent #345) (paragraph (:begin 2461 :end 2656 :contents-begin 2461 :contents-end 2655 :post-blank 1 :post-affiliated 2461 :mode planning :granularity nil :parent #348) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #351)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 2514 :end 2565 :contents-begin 2544 :contents-end 2563 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 2551 :end 2563 :use-brackets-p nil :contents-begin 2552 :contents-end 2563 :post-blank 0 :parent #355) #("settings.py" 0 11 (:parent #359)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #351))) (fixed-width (:begin 2656 :end 2686 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 2656 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2686 :end 2764 :contents-begin 2686 :contents-end 2763 :post-blank 1 :post-affiliated 2686 :mode nil :granularity nil :parent #348) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #353))) (fixed-width (:begin 2764 :end 2847 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 2764 :mode nil :granularity nil :parent #348)) (paragraph (:begin 2847 :end 2926 :contents-begin 2847 :contents-end 2926 :post-blank 0 :post-affiliated 2847 :mode nil :granularity nil :parent #348) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #355))))) (headline (:raw-value "Run gn-proxy" :begin 2927 :end 3118 :pre-blank 1 :contents-begin 2943 :contents-end 3117 :robust-begin 2945 :robust-end 3115 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2927 :title (#("Run gn-proxy" 0 12 (:parent #346))) :mode nil :granularity nil :parent #338) (section (:begin 2943 :end 3118 :contents-begin 2943 :contents-end 3117 :robust-begin 2943 :robust-end 3115 :post-blank 1 :post-affiliated 2943 :mode section :granularity nil :parent #346) (paragraph (:begin 2943 :end 3117 :contents-begin 2943 :contents-end 3117 :post-blank 0 :post-affiliated 2943 :mode planning :granularity nil :parent #349) #("GeneNetwork requires a separate gn-proxy server which handles\nauthorisation and access control. For instructions see the " 0 121 (:parent #352)) (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 3064 :end 3115 :contents-begin 3107 :contents-end 3113 :post-blank 0 :parent #352) #("README" 0 6 (:parent #356))) #(".\n" 0 2 (:parent #352))))) (headline (:raw-value "Run Redis" :begin 3118 :end 3223 :pre-blank 1 :contents-begin 3131 :contents-end 3222 :robust-begin 3133 :robust-end 3220 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3118 :title (#("Run Redis" 0 9 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 3131 :end 3223 :contents-begin 3131 :contents-end 3222 :robust-begin 3131 :robust-end 3220 :post-blank 1 :post-affiliated 3131 :mode section :granularity nil :parent #347) (paragraph (:begin 3131 :end 3222 :contents-begin 3131 :contents-end 3222 :post-blank 0 :post-affiliated 3131 :mode planning :granularity nil :parent #350) #("Redis part of GN2 deployment and will be started by the ./bin/genenetwork2\nstartup script.\n" 0 91 (:parent #353))))) (headline (:raw-value "Run MariaDB server" :begin 3223 :end 6322 :pre-blank 0 :contents-begin 3244 :contents-end 6321 :robust-begin 3246 :robust-end 6319 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3223 :title (#("Run MariaDB server" 0 18 (:parent #348))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MariaDB with GNU GUIx" :begin 3244 :end 4771 :pre-blank 1 :contents-begin 3278 :contents-end 4770 :robust-begin 3280 :robust-end 4768 :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 3244 :title (#("Install MariaDB with GNU GUIx" 0 29 (:parent #351))) :mode section :granularity nil :parent #348) (section (:begin 3278 :end 4771 :contents-begin 3278 :contents-end 4770 :robust-begin 3278 :robust-end 4768 :post-blank 1 :post-affiliated 3278 :mode section :granularity nil :parent #351) (paragraph (:begin 3278 :end 3415 :contents-begin 3278 :contents-end 3414 :post-blank 1 :post-affiliated 3278 :mode planning :granularity nil :parent #354) #("These are the steps you can take to install a fresh installation of\nmariadb (which comes as part of the GNU Guix genenetwork2 install).\n" 0 136 (:parent #357))) (paragraph (:begin 3415 :end 3451 :contents-begin 3415 :contents-end 3450 :post-blank 1 :post-affiliated 3415 :mode nil :granularity nil :parent #354) #("As root configure the Guix profile\n" 0 35 (:parent #358))) (fixed-width (:begin 3451 :end 3487 :value ". ~/opt/genenetwork2/etc/profile" :post-blank 2 :post-affiliated 3451 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3487 :end 3508 :contents-begin 3487 :contents-end 3507 :post-blank 1 :post-affiliated 3487 :mode nil :granularity nil :parent #354) #("and run for example\n" 0 20 (:parent #360))) (src-block (:language "bash" :switches nil :parameters nil :begin 3508 :end 3996 :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 3508 :mode nil :granularity nil :parent #354)) (paragraph (:begin 3996 :end 4044 :contents-begin 3996 :contents-end 4043 :post-blank 1 :post-affiliated 3996 :mode nil :granularity nil :parent #354) #("If you want to run as root you may have to set\n" 0 47 (:parent #362))) (fixed-width (:begin 4044 :end 4084 :value "/etc/my.cnf\n[mariadbd]\nuser=root" :post-blank 2 :post-affiliated 4044 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4084 :end 4106 :contents-begin 4084 :contents-end 4105 :post-blank 1 :post-affiliated 4084 :mode nil :granularity nil :parent #354) #("You also need to set\n" 0 21 (:parent #364))) (fixed-width (:begin 4106 :end 4129 :value "ft_min_word_len = 3" :post-blank 2 :post-affiliated 4106 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4129 :end 4209 :contents-begin 4129 :contents-end 4208 :post-blank 1 :post-affiliated 4129 :mode nil :granularity nil :parent #354) #("To make sure word text searches (shh) work and rebuild the tables if\nrequired.\n" 0 79 (:parent #366))) (paragraph (:begin 4209 :end 4278 :contents-begin 4209 :contents-end 4277 :post-blank 1 :post-affiliated 4209 :mode nil :granularity nil :parent #354) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #367))) (fixed-width (:begin 4278 :end 4393 :value "mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log" :post-blank 2 :post-affiliated 4278 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4393 :end 4471 :contents-begin 4393 :contents-end 4470 :post-blank 1 :post-affiliated 4393 :mode nil :granularity nil :parent #354) #("Other tips are that Guix installs mariadbd in your profile, so this may work\n" 0 77 (:parent #369))) (fixed-width (:begin 4471 :end 4581 :value "/home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb" :post-blank 2 :post-affiliated 4471 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4581 :end 4608 :contents-begin 4581 :contents-end 4607 :post-blank 1 :post-affiliated 4581 :mode nil :granularity nil :parent #354) #("When you get errors like:\n" 0 26 (:parent #371))) (fixed-width (:begin 4608 :end 4722 :value "qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 4608 :mode nil :granularity nil :parent #354)) (paragraph (:begin 4722 :end 4743 :contents-begin 4722 :contents-end 4742 :post-blank 1 :post-affiliated 4722 :mode nil :granularity nil :parent #354) #("you may need to set\n" 0 20 (:parent #373))) (fixed-width (:begin 4743 :end 4770 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 4743 :mode nil :granularity nil :parent #354)))) (headline (:raw-value "Load the small database in MySQL" :begin 4771 :end 6322 :pre-blank 1 :contents-begin 4808 :contents-end 6321 :robust-begin 4810 :robust-end 6319 :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 4771 :title (#("Load the small database in MySQL" 0 32 (:parent #352))) :mode nil :granularity nil :parent #348) (section (:begin 4808 :end 6322 :contents-begin 4808 :contents-end 6321 :robust-begin 4808 :robust-end 6319 :post-blank 1 :post-affiliated 4808 :mode section :granularity nil :parent #352) (paragraph (:begin 4808 :end 5115 :contents-begin 4808 :contents-end 5114 :post-blank 1 :post-affiliated 4808 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 4971 :end 4978 :use-brackets-p nil :contents-begin 4972 :contents-end 4978 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #362))) (subscript (:begin 4978 :end 4980 :use-brackets-p nil :contents-begin 4979 :contents-end 4980 :post-blank 0 :parent #358) #("s" 0 1 (:parent #363))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #358)) (subscript (:begin 5056 :end 5063 :use-brackets-p nil :contents-begin 5057 :contents-end 5063 :post-blank 0 :parent #358) #("webqtl" 0 6 (:parent #365))) (subscript (:begin 5063 :end 5069 :use-brackets-p nil :contents-begin 5064 :contents-end 5069 :post-blank 0 :parent #358) #("plant" 0 5 (:parent #366))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #358))) (paragraph (:begin 5115 :end 5143 :contents-begin 5115 :contents-end 5142 :post-blank 1 :post-affiliated 5115 :mode nil :granularity nil :parent #355) #("Download one database from\n" 0 27 (:parent #359))) (paragraph (:begin 5143 :end 5224 :contents-begin 5143 :contents-end 5223 :post-blank 1 :post-affiliated 5143 :mode nil :granularity nil :parent #355) (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 5143 :end 5222 :contents-begin nil :contents-end nil :post-blank 0 :parent #360)) #("\n" 0 1 (:parent #360))) (paragraph (:begin 5224 :end 5293 :contents-begin 5224 :contents-end 5292 :post-blank 1 :post-affiliated 5224 :mode nil :granularity nil :parent #355) #("After installation unzip the database binary in the MySQL directory\n" 0 68 (:parent #361))) (src-block (:language "sh" :switches nil :parameters nil :begin 5293 :end 5435 :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 5293 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5435 :end 5482 :contents-begin 5435 :contents-end 5481 :post-blank 1 :post-affiliated 5435 :mode nil :granularity nil :parent #355) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5482 :end 5515 :value "mysql_upgrade -u root --force" :post-blank 2 :post-affiliated 5482 :mode nil :granularity nil :parent #355)) (fixed-width (:begin 5515 :end 5532 :value "myslq -u root" :post-blank 2 :post-affiliated 5515 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5532 :end 5537 :contents-begin 5532 :contents-end 5536 :post-blank 1 :post-affiliated 5532 :mode nil :granularity nil :parent #355) #("and\n" 0 4 (:parent #366))) (fixed-width (:begin 5537 :end 5763 :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 5537 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5763 :end 5828 :contents-begin 5763 :contents-end 5827 :post-blank 1 :post-affiliated 5763 :mode nil :granularity nil :parent #355) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #368))) (fixed-width (:begin 5828 :end 5919 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'webqtl';" :post-blank 2 :post-affiliated 5828 :mode nil :granularity nil :parent #355)) (paragraph (:begin 5919 :end 6026 :contents-begin 5919 :contents-end 6025 :post-blank 1 :post-affiliated 5919 :mode nil :granularity nil :parent #355) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #370))) (paragraph (:begin 6026 :end 6189 :contents-begin 6026 :contents-end 6188 :post-blank 1 :post-affiliated 6026 :mode nil :granularity nil :parent #355) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #371))) (paragraph (:begin 6189 :end 6321 :contents-begin 6189 :contents-end 6321 :post-blank 0 :post-affiliated 6189 :mode nil :granularity nil :parent #355) #("Note for the plant database you can rename it to db" 0 51 (:parent #372)) (subscript (:begin 6240 :end 6247 :use-brackets-p nil :contents-begin 6241 :contents-end 6247 :post-blank 0 :parent #372) #("webqtl" 0 6 (:parent #376))) (subscript (:begin 6247 :end 6249 :use-brackets-p nil :contents-begin 6248 :contents-end 6249 :post-blank 0 :parent #372) #("s" 0 1 (:parent #377))) #(", or\nchange the settings in etc/default" 0 39 (:parent #372)) (subscript (:begin 6288 :end 6301 :use-brackets-p nil :contents-begin 6289 :contents-end 6300 :post-blank 1 :parent #372) #("settings.py" 0 11 (:parent #379))) #("to match your path.\n" 0 20 (:parent #372)))))) (headline (:raw-value "Get genotype files" :begin 6322 :end 6564 :pre-blank 1 :contents-begin 6344 :contents-end 6563 :robust-begin 6346 :robust-end 6561 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6322 :title (#("Get genotype files" 0 18 (:parent #349))) :mode nil :granularity nil :parent #338) (section (:begin 6344 :end 6564 :contents-begin 6344 :contents-end 6563 :robust-begin 6344 :robust-end 6561 :post-blank 1 :post-affiliated 6344 :mode section :granularity nil :parent #349) (paragraph (:begin 6344 :end 6483 :contents-begin 6344 :contents-end 6482 :post-blank 1 :post-affiliated 6344 :mode planning :granularity nil :parent #352) #("The script looks for genotype files. You can find them in\n" 0 58 (:parent #355)) (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 6402 :end 6481 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #("\n" 0 1 (:parent #355))) (src-block (:language "sh" :switches nil :parameters nil :begin 6483 :end 6563 :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 6483 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "GN2 Dependency Graph" :begin 6564 :end 6728 :pre-blank 1 :contents-begin 6588 :contents-end 6727 :robust-begin 6590 :robust-end 6725 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6564 :title (#("GN2 Dependency Graph" 0 20 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 6588 :end 6728 :contents-begin 6588 :contents-end 6727 :robust-begin 6588 :robust-end 6725 :post-blank 1 :post-affiliated 6588 :mode section :granularity nil :parent #350) (paragraph (:begin 6588 :end 6649 :contents-begin 6588 :contents-end 6648 :post-blank 1 :post-affiliated 6588 :mode planning :granularity nil :parent #353) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #356))) (paragraph (:begin 6649 :end 6727 :contents-begin 6679 :contents-end 6727 :post-blank 0 :post-affiliated 6679 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #353) (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 6679 :end 6726 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #("\n" 0 1 (:parent #357))))) (headline (:raw-value "Working with the GN2 source code" :begin 6728 :end 6790 :pre-blank 1 :contents-begin 6764 :contents-end 6789 :robust-begin 6766 :robust-end 6787 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6728 :title (#("Working with the GN2 source code" 0 32 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 6764 :end 6790 :contents-begin 6764 :contents-end 6789 :robust-begin 6764 :robust-end 6787 :post-blank 1 :post-affiliated 6764 :mode section :granularity nil :parent #351) (paragraph (:begin 6764 :end 6789 :contents-begin 6764 :contents-end 6789 :post-blank 0 :post-affiliated 6764 :mode planning :granularity nil :parent #354) #("See " 0 4 (:parent #357)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6768 :end 6787 :contents-begin nil :contents-end nil :post-blank 0 :parent #357)) #(".\n" 0 2 (:parent #357))))) (headline (:raw-value "Read more" :begin 6790 :end 6940 :pre-blank 1 :contents-begin 6803 :contents-end 6939 :robust-begin 6805 :robust-end 6937 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6790 :title (#("Read more" 0 9 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 6803 :end 6940 :contents-begin 6803 :contents-end 6939 :robust-begin 6803 :robust-end 6937 :post-blank 1 :post-affiliated 6803 :mode section :granularity nil :parent #352) (paragraph (:begin 6803 :end 6939 :contents-begin 6803 :contents-end 6939 :post-blank 0 :post-affiliated 6803 :mode planning :granularity nil :parent #355) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #358)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 6858 :end 6878 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #358))))) (headline (:raw-value "Trouble shooting" :begin 6940 :end 9390 :pre-blank 1 :contents-begin 6960 :contents-end 9389 :robust-begin 6962 :robust-end 9387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6940 :title (#("Trouble shooting" 0 16 (:parent #353))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6960 :end 7494 :pre-blank 1 :contents-begin 7000 :contents-end 7494 :robust-begin 7002 :robust-end 7492 :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 6960 :title (#("ImportError: No module named jinja2" 0 35 (:parent #356))) :mode section :granularity nil :parent #353) (section (:begin 7000 :end 7494 :contents-begin 7000 :contents-end 7494 :robust-begin 7000 :robust-end 7492 :post-blank 0 :post-affiliated 7000 :mode section :granularity nil :parent #356) (paragraph (:begin 7000 :end 7235 :contents-begin 7000 :contents-end 7234 :post-blank 1 :post-affiliated 7000 :mode planning :granularity nil :parent #359) #("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 #362)) (subscript (:begin 7167 :end 7173 :use-brackets-p nil :contents-begin 7168 :contents-end 7172 :post-blank 1 :parent #362) #("PATH" 0 4 (:parent #366))) #("and R" 0 5 (:parent #362)) (subscript (:begin 7178 :end 7183 :use-brackets-p nil :contents-begin 7179 :contents-end 7183 :post-blank 0 :parent #362) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7183 :end 7189 :use-brackets-p nil :contents-begin 7184 :contents-end 7188 :post-blank 1 :parent #362) #("SITE" 0 4 (:parent #369))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #362))) (fixed-width (:begin 7235 :end 7266 :value "guix package --search-paths" :post-blank 2 :post-affiliated 7235 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7266 :end 7282 :contents-begin 7266 :contents-end 7281 :post-blank 1 :post-affiliated 7266 :mode nil :granularity nil :parent #359) #("On one system:\n" 0 15 (:parent #364))) (fixed-width (:begin 7282 :end 7470 :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 7282 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7470 :end 7494 :contents-begin 7470 :contents-end 7494 :post-blank 0 :post-affiliated 7470 :mode nil :granularity nil :parent #359) #("and perhaps a few more.\n" 0 24 (:parent #366))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 7494 :end 7990 :pre-blank 1 :contents-begin 7603 :contents-end 7989 :robust-begin 7605 :robust-end 7987 :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 7494 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #357)) (subscript (:begin 7537 :end 7542 :use-brackets-p nil :contents-begin 7538 :contents-end 7542 :post-blank 0 :parent #357) #("data" 0 4 (:parent #399))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #357)) (subscript (:begin 7585 :end 7591 :use-brackets-p nil :contents-begin 7586 :contents-end 7591 :post-blank 0 :parent #357) #("files" 0 5 (:parent #401))) #("/genotype'" 0 10 (:parent #357))) :mode nil :granularity nil :parent #353) (section (:begin 7603 :end 7990 :contents-begin 7603 :contents-end 7989 :robust-begin 7603 :robust-end 7987 :post-blank 1 :post-affiliated 7603 :mode section :granularity nil :parent #357) (paragraph (:begin 7603 :end 7825 :contents-begin 7603 :contents-end 7824 :post-blank 1 :post-affiliated 7603 :mode planning :granularity nil :parent #360) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #363)) (subscript (:begin 7652 :end 7657 :use-brackets-p nil :contents-begin 7653 :contents-end 7657 :post-blank 0 :parent #363) #("data" 0 4 (:parent #367))) #(". 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 #363)) (subscript (:begin 7781 :end 7794 :use-brackets-p nil :contents-begin 7782 :contents-end 7793 :post-blank 1 :parent #363) #("settings.py" 0 11 (:parent #369))) #("(see above in\nthis document).\n" 0 30 (:parent #363))) (paragraph (:begin 7825 :end 7899 :contents-begin 7825 :contents-end 7898 :post-blank 1 :post-affiliated 7825 :mode nil :granularity nil :parent #360) #("You can use the GENENETWORK" 0 27 (:parent #364)) (subscript (:begin 7852 :end 7859 :use-brackets-p nil :contents-begin 7853 :contents-end 7858 :post-blank 1 :parent #364) #("FILES" 0 5 (:parent #368))) #("switch to set the datadir, for example\n" 0 39 (:parent #364))) (fixed-width (:begin 7899 :end 7989 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 7899 :mode nil :granularity nil :parent #360)))) (headline (:raw-value "Can't run a module" :begin 7990 :end 8224 :pre-blank 1 :contents-begin 8013 :contents-end 8224 :robust-begin 8015 :robust-end 8222 :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 7990 :title (#("Can't run a module" 0 18 (:parent #358))) :mode nil :granularity nil :parent #353) (section (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :robust-begin 8013 :robust-end 8222 :post-blank 0 :post-affiliated 8013 :mode section :granularity nil :parent #358) (paragraph (:begin 8013 :end 8224 :contents-begin 8013 :contents-end 8224 :post-blank 0 :post-affiliated 8013 :mode planning :granularity nil :parent #361) #("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 #364))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 8224 :end 8725 :pre-blank 1 :contents-begin 8256 :contents-end 8724 :robust-begin 8258 :robust-end 8722 :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 8224 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #359))) :mode nil :granularity nil :parent #353) (section (:begin 8256 :end 8725 :contents-begin 8256 :contents-end 8724 :robust-begin 8256 :robust-end 8722 :post-blank 1 :post-affiliated 8256 :mode section :granularity nil :parent #359) (paragraph (:begin 8256 :end 8268 :contents-begin 8256 :contents-end 8267 :post-blank 1 :post-affiliated 8256 :mode planning :granularity nil :parent #362) #("This error\n" 0 11 (:parent #365))) (fixed-width (:begin 8268 :end 8348 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 8268 :mode nil :granularity nil :parent #362)) (paragraph (:begin 8348 :end 8479 :contents-begin 8348 :contents-end 8478 :post-blank 1 :post-affiliated 8348 :mode nil :granularity nil :parent #362) #("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 #367))) (paragraph (:begin 8479 :end 8724 :contents-begin 8479 :contents-end 8724 :post-blank 0 :post-affiliated 8479 :mode nil :granularity nil :parent #362) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #368)) (subscript (:begin 8542 :end 8547 :use-brackets-p nil :contents-begin 8543 :contents-end 8547 :post-blank 0 :parent #368) #("LIBS" 0 4 (:parent #372))) (subscript (:begin 8547 :end 8552 :use-brackets-p nil :contents-begin 8548 :contents-end 8552 :post-blank 0 :parent #368) #("SITE" 0 4 (:parent #373))) #(". 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 #368))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 8725 :end 9390 :pre-blank 1 :contents-begin 8777 :contents-end 9389 :robust-begin 8779 :robust-end 9387 :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 8725 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #360))) :mode nil :granularity nil :parent #353) (section (:begin 8777 :end 9390 :contents-begin 8777 :contents-end 9389 :robust-begin 8777 :robust-end 9387 :post-blank 1 :post-affiliated 8777 :mode section :granularity nil :parent #360) (paragraph (:begin 8777 :end 8798 :contents-begin 8777 :contents-end 8797 :post-blank 1 :post-affiliated 8777 :mode planning :granularity nil :parent #363) #("The following error\n" 0 20 (:parent #366))) (fixed-width (:begin 8798 :end 8993 :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 8798 :mode nil :granularity nil :parent #363)) (paragraph (:begin 8993 :end 9151 :contents-begin 8993 :contents-end 9150 :post-blank 1 :post-affiliated 8993 :mode nil :granularity nil :parent #363) #("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 #368))) (fixed-width (:begin 9151 :end 9173 :value "mysql -h localhost" :post-blank 2 :post-affiliated 9151 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9173 :end 9230 :contents-begin 9173 :contents-end 9229 :post-blank 1 :post-affiliated 9173 :mode nil :granularity nil :parent #363) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #370))) (fixed-width (:begin 9230 :end 9252 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 9230 :mode nil :granularity nil :parent #363)) (paragraph (:begin 9252 :end 9323 :contents-begin 9252 :contents-end 9322 :post-blank 1 :post-affiliated 9252 :mode nil :granularity nil :parent #363) #("if that works run genenetwork after setting SQL" 0 47 (:parent #372)) (subscript (:begin 9299 :end 9304 :use-brackets-p nil :contents-begin 9300 :contents-end 9303 :post-blank 1 :parent #372) #("URI" 0 3 (:parent #376))) #("to something like\n" 0 18 (:parent #372))) (fixed-width (:begin 9323 :end 9389 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 9323 :mode nil :granularity nil :parent #363))))) (headline (:raw-value "NOTES" :begin 9390 :end 10302 :pre-blank 1 :contents-begin 9399 :contents-end 10302 :robust-begin 9401 :robust-end 10300 :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 9390 :title (#("NOTES" 0 5 (:parent #354))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Deploying GN2 official" :begin 9399 :end 10302 :pre-blank 1 :contents-begin 9426 :contents-end 10302 :robust-begin 9428 :robust-end 10300 :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 9399 :title (#("Deploying GN2 official" 0 22 (:parent #357))) :mode section :granularity nil :parent #354) (section (:begin 9426 :end 10302 :contents-begin 9426 :contents-end 10302 :robust-begin 9426 :robust-end 10300 :post-blank 0 :post-affiliated 9426 :mode section :granularity nil :parent #357) (paragraph (:begin 9426 :end 9482 :contents-begin 9426 :contents-end 9481 :post-blank 1 :post-affiliated 9426 :mode planning :granularity nil :parent #360) #("Let's see how fast we can deploy a second copy of GN2.\n" 0 55 (:parent #363))) (plain-list (:type unordered :begin 9482 :end 10302 :contents-begin 9482 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 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"- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 9482 :tag nil :mode item :granularity nil :parent #364) (paragraph (:begin 9488 :end 9501 :contents-begin 9488 :contents-end 9501 :post-blank 0 :post-affiliated 9488 :mode nil :granularity nil :parent #367) #("Base install\n" 0 13 (:parent #370))) (plain-list (:type unordered :begin 9501 :end 10302 :contents-begin 9501 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :post-blank 0 :post-affiliated 9501 :mode nil :granularity nil :parent #367) (item (:bullet "+ " :begin 9501 :end 9562 :contents-begin 9509 :contents-end 9562 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil 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"- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 "- " nil "[ ]" nil 10302)) :pre-blank 0 :post-blank 0 :post-affiliated 10124 :tag nil :mode item :granularity nil :parent #382) (paragraph (:begin 10134 :end 10188 :contents-begin 10134 :contents-end 10188 :post-blank 0 :post-affiliated 10134 :mode nil :granularity nil :parent #388) #("update database (see gn-services/services/mariadb.md)\n" 0 54 (:parent #391)))) (item (:bullet "- " :begin 10188 :end 10211 :contents-begin 10198 :contents-end 10211 :checkbox off :counter nil :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 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(paragraph (:begin 10256 :end 10277 :contents-begin 10256 :contents-end 10277 :post-blank 0 :post-affiliated 10256 :mode nil :granularity nil :parent #381) #("install genenetwork3\n" 0 21 (:parent #384))) (plain-list (:type unordered :begin 10277 :end 10302 :contents-begin 10277 :contents-end 10302 :structure ((9482 0 "- " nil "[ ]" nil 10302) (9501 2 "+ " nil "[ ]" nil 9562) (9562 2 "+ " nil "[ ]" nil 9840) (9591 4 "- " nil "[ ]" nil 9635) (9635 4 "- " nil "[ ]" nil 9762) (9762 4 "- " nil "[ ]" nil 9840) (9840 2 "+ " nil "[ ]" nil 9886) (9886 2 "+ " nil "[ ]" nil 9986) (9908 4 "- " nil "[ ]" nil 9933) (9933 4 "- " nil "[ ]" nil 9960) (9960 4 "- " nil "[ ]" nil 9986) (9986 2 "+ " nil "[ ]" nil 10211) (10044 4 "- " nil "[ ]" nil 10069) (10069 4 "- " nil "[ ]" nil 10097) (10097 4 "- " nil "[ ]" nil 10124) (10124 4 "- " nil "[ ]" nil 10188) (10188 4 "- " nil "[ ]" nil 10211) (10211 2 "+ " nil "[ ]" nil 10227) (10227 2 "+ " nil "[ ]" nil 10248) (10248 2 "+ " nil "[ ]" nil 10302) (10277 4 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nil :mode item :granularity nil :parent #385) (paragraph (:begin 10287 :end 10302 :contents-begin 10287 :contents-end 10302 :post-blank 0 :post-affiliated 10287 :mode nil :granularity nil :parent #388) #("add to systemd\n" 0 15 (:parent #391))))))))))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #)) org-export-as(html nil nil t nil) org-export-to-buffer(html "*Org HTML Export*" nil nil nil t nil #f(compiled-function () #)) org-html-export-as-html(nil nil nil t) (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (let ((temp-buffer (generate-new-buffer " *temp*" t))) (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (pipe-stdin-into-current-buffer) (org-html-export-as-html nil nil nil t) (princ (buffer-string))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer))))) eval-buffer(# nil "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t) #f(compiled-function (buffer file) #)(# "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") load-with-code-conversion("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el" nil t #f(compiled-function (buffer file) #)) command-line--load-script("/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el") command-line-1(("-scriptload" "/gnu/store/0h55qvzlzmvwgigk6nrzcc6s2g30ddm0-org2html.el")) command-line() normal-top-level()