Error: user-error ("Unable to resolve link: \"introduction\"")
mapbacktrace(#f(compiled-function (evald func args flags) #))
debug-early-backtrace()
debug-early(error (user-error "Unable to resolve link: \"introduction\""))
signal(user-error ("Unable to resolve link: \"introduction\""))
user-error("Unable to resolve link: %S" "introduction")
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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1364 :end 1438 :contents-begin 1426 :contents-end 1436 :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 1521 :end 1871 :contents-begin 1521 :contents-end 1870 :post-blank 1 :post-affiliated 1521 :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 1739 :end 1815 :contents-begin 1793 :contents-end 1812 :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 1819 :end 1868 :contents-begin 1858 :contents-end 1866 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 1871 :end 2006 :contents-begin 1871 :contents-end 2006 :post-blank 0 :post-affiliated 1871 :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 1957 :end 2004 :contents-begin 1982 :contents-end 2002 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2007 :end 3390 :pre-blank 1 :contents-begin 2018 :contents-end 3389 :robust-begin 2020 :robust-end 3387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2007 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2018 :end 2382 :contents-begin 2018 :contents-end 2381 :robust-begin 2018 :robust-end 2379 :post-blank 1 :post-affiliated 2018 :mode section :granularity nil :parent #178) (paragraph (:begin 2018 :end 2381 :contents-begin 2018 :contents-end 2381 :post-blank 0 :post-affiliated 2018 :mode planning :granularity nil :parent #181) #("The quickest way to install GN2 is by using a binary installation\n(tarball or Docker image). These installations are bundled by GNU\nGuix and include all dependencies. You can install GeneNetwork on most\nLinux distributions, including Debian, Ubuntu, Fedora and CentOS,\nprovided you have administrator privileges (root). The alternative is\na Docker installation.\n" 0 363 (:parent #184)))) (headline (:raw-value "Tarball" :begin 2382 :end 3035 :pre-blank 1 :contents-begin 2394 :contents-end 3034 :robust-begin 2396 :robust-end 3032 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2382 :title (#("Tarball" 0 7 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2394 :end 3035 :contents-begin 2394 :contents-end 3034 :robust-begin 2394 :robust-end 3032 :post-blank 1 :post-affiliated 2394 :mode section :granularity nil :parent #182) (paragraph (:begin 2394 :end 2541 :contents-begin 2394 :contents-end 2540 :post-blank 1 :post-affiliated 2394 :mode planning :granularity nil :parent #185) #("Download the ~800Mb tarball from\n" 0 33 (:parent #188)) (link (:type "http" :path "//files.genenetwork.org/software/binary_tarball/" :format bracket :raw-link "http://files.genenetwork.org/software/binary_tarball/" :application nil :search-option nil :begin 2427 :end 2484 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(". Validate the checksum and\nunpack to root, for example\n" 0 56 (:parent #188))) (fixed-width (:begin 2541 :end 2643 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2541 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2643 :end 2691 :contents-begin 2643 :contents-end 2690 :post-blank 1 :post-affiliated 2643 :mode nil :granularity nil :parent #185) #("Now you shoud be able to start the server with\n" 0 47 (:parent #190))) (fixed-width (:begin 2691 :end 2729 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2691 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2729 :end 2856 :contents-begin 2729 :contents-end 2855 :post-blank 1 :post-affiliated 2729 :mode nil :granularity nil :parent #185) #("When the server stops with a MySQL error " 0 41 (:parent #192)) (link (:type "custom-id" :path "run-mysql-server" :format bracket :raw-link "#run-mysql-server" :application nil :search-option nil :begin 2770 :end 2809 :contents-begin 2791 :contents-end 2807 :post-blank 0 :parent #192) #("Run MySQL server" 0 16 (:parent #196))) #("\nand set SQL" 0 12 (:parent #192)) (subscript (:begin 2821 :end 2826 :use-brackets-p nil :contents-begin 2822 :contents-end 2825 :post-blank 1 :parent #192) #("URI" 0 3 (:parent #198))) #("to point at it. For example:\n" 0 29 (:parent #192))) (fixed-width (:begin 2856 :end 2923 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 2856 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2923 :end 3034 :contents-begin 2923 :contents-end 3034 :post-blank 0 :post-affiliated 2923 :mode nil :granularity nil :parent #185) #("See also " 0 9 (:parent #194)) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 2932 :end 3032 :contents-begin 2983 :contents-end 3030 :post-blank 0 :parent #194) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #198))) #(".\n" 0 2 (:parent #194))))) (headline (:raw-value "Docker" :begin 3035 :end 3244 :pre-blank 1 :contents-begin 3046 :contents-end 3243 :robust-begin 3048 :robust-end 3241 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3035 :title (#("Docker" 0 6 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 3046 :end 3244 :contents-begin 3046 :contents-end 3243 :robust-begin 3046 :robust-end 3241 :post-blank 1 :post-affiliated 3046 :mode section :granularity nil :parent #183) (paragraph (:begin 3046 :end 3243 :contents-begin 3046 :contents-end 3243 :post-blank 0 :post-affiliated 3046 :mode planning :granularity nil :parent #186) #("Docker images are also available through\n" 0 41 (:parent #189)) (link (:type "http" :path "//files.genenetwork.org/software/" :format bracket :raw-link "http://files.genenetwork.org/software/" :application nil :search-option nil :begin 3087 :end 3129 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(". Validate the checksum and run\nwith " 0 37 (:parent #189)) (link (:type "https" :path "//docs.docker.com/engine/reference/commandline/load/" :format bracket :raw-link "https://docs.docker.com/engine/reference/commandline/load/" :application nil :search-option nil :begin 3166 :end 3241 :contents-begin 3228 :contents-end 3239 :post-blank 0 :parent #189) #("Docker load" 0 11 (:parent #195))) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "With source" :begin 3244 :end 3390 :pre-blank 1 :contents-begin 3260 :contents-end 3389 :robust-begin 3262 :robust-end 3387 :level 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 (#("With source" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 3260 :end 3390 :contents-begin 3260 :contents-end 3389 :robust-begin 3260 :robust-end 3387 :post-blank 1 :post-affiliated 3260 :mode section :granularity nil :parent #184) (paragraph (:begin 3260 :end 3389 :contents-begin 3260 :contents-end 3389 :post-blank 0 :post-affiliated 3260 :mode planning :granularity nil :parent #187) #("For more elaborate installation instructions on deploying GeneNetwork from\nsource see " 0 86 (:parent #190)) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 3346 :end 3387 :contents-begin 3368 :contents-end 3385 :post-blank 0 :parent #190) #("Source deployment" 0 17 (:parent #194))) #(".\n" 0 2 (:parent #190)))))) (headline (:raw-value "Running GN2" :begin 3390 :end 3871 :pre-blank 1 :contents-begin 3405 :contents-end 3870 :robust-begin 3407 :robust-end 3868 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3390 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 3405 :end 3871 :contents-begin 3405 :contents-end 3870 :robust-begin 3405 :robust-end 3868 :post-blank 1 :post-affiliated 3405 :mode section :granularity nil :parent #179) (paragraph (:begin 3405 :end 3600 :contents-begin 3405 :contents-end 3599 :post-blank 1 :post-affiliated 3405 :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 3458 :end 3509 :contents-begin 3488 :contents-end 3507 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 3495 :end 3507 :use-brackets-p nil :contents-begin 3496 :contents-end 3507 :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 3600 :end 3630 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3600 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3630 :end 3708 :contents-begin 3630 :contents-end 3707 :post-blank 1 :post-affiliated 3630 :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 3708 :end 3791 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3708 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3791 :end 3870 :contents-begin 3791 :contents-end 3870 :post-blank 0 :post-affiliated 3791 :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 MySQL server" :begin 3871 :end 5896 :pre-blank 0 :contents-begin 3890 :contents-end 5895 :robust-begin 3892 :robust-end 5893 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3871 :title (#("Run MySQL server" 0 16 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 3890 :end 4364 :pre-blank 1 :contents-begin 3922 :contents-end 4363 :robust-begin 3924 :robust-end 4361 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3890 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 3922 :end 4364 :contents-begin 3922 :contents-end 4363 :robust-begin 3922 :robust-end 4361 :post-blank 1 :post-affiliated 3922 :mode section :granularity nil :parent #183) (paragraph (:begin 3922 :end 4057 :contents-begin 3922 :contents-end 4056 :post-blank 1 :post-affiliated 3922 :mode planning :granularity nil :parent #186) #("These are the steps you can take to install a fresh installation of\nmysql (which comes as part of the GNU Guix genenetwork2 install).\n" 0 134 (:parent #189))) (paragraph (:begin 4057 :end 4084 :contents-begin 4057 :contents-end 4083 :post-blank 1 :post-affiliated 4057 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #190))) (fixed-width (:begin 4084 :end 4332 :value " adduser mysql && addgroup mysql\n mysqld --datadir=/var/mysql --initialize-insecure\n mkdir -p /var/run/mysqld\n chown mysql.mysql ~/mysql /var/run/mysqld\n su mysql -c mysqld --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" :post-blank 2 :post-affiliated 4084 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4332 :end 4363 :contents-begin 4332 :contents-end 4363 :post-blank 0 :post-affiliated 4332 :mode nil :granularity nil :parent #186) #("/etc/my.cnf\n[mysqld]\nuser=root\n" 0 31 (:parent #192))))) (headline (:raw-value "Load the small database in MySQL" :begin 4364 :end 5896 :pre-blank 1 :contents-begin 4401 :contents-end 5895 :robust-begin 4403 :robust-end 5893 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4364 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 4401 :end 5896 :contents-begin 4401 :contents-end 5895 :robust-begin 4401 :robust-end 5893 :post-blank 1 :post-affiliated 4401 :mode section :granularity nil :parent #184) (paragraph (:begin 4401 :end 4708 :contents-begin 4401 :contents-end 4707 :post-blank 1 :post-affiliated 4401 :mode planning :granularity nil :parent #187) #("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 #190)) (subscript (:begin 4564 :end 4571 :use-brackets-p nil :contents-begin 4565 :contents-end 4571 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 4571 :end 4573 :use-brackets-p nil :contents-begin 4572 :contents-end 4573 :post-blank 0 :parent #190) #("s" 0 1 (:parent #195))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #190)) (subscript (:begin 4649 :end 4656 :use-brackets-p nil :contents-begin 4650 :contents-end 4656 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 4656 :end 4662 :use-brackets-p nil :contents-begin 4657 :contents-end 4662 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 4708 :end 4736 :contents-begin 4708 :contents-end 4735 :post-blank 1 :post-affiliated 4708 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 4736 :end 4784 :contents-begin 4736 :contents-end 4783 :post-blank 1 :post-affiliated 4736 :mode nil :granularity nil :parent #187) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4736 :end 4782 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 4784 :end 4843 :contents-begin 4784 :contents-end 4842 :post-blank 1 :post-affiliated 4784 :mode nil :granularity nil :parent #187) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4784 :end 4841 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4843 :end 4862 :contents-begin 4843 :contents-end 4861 :post-blank 1 :post-affiliated 4843 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 4862 :end 4933 :contents-begin 4862 :contents-end 4932 :post-blank 1 :post-affiliated 4862 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 4933 :end 5034 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4933 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5034 :end 5081 :contents-begin 5034 :contents-end 5080 :post-blank 1 :post-affiliated 5034 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5081 :end 5098 :value "myslq -u root" :post-blank 2 :post-affiliated 5081 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5098 :end 5103 :contents-begin 5098 :contents-end 5102 :post-blank 1 :post-affiliated 5098 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 5103 :end 5329 :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 5103 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5329 :end 5394 :contents-begin 5329 :contents-end 5393 :post-blank 1 :post-affiliated 5329 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 5394 :end 5493 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5394 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5493 :end 5600 :contents-begin 5493 :contents-end 5599 :post-blank 1 :post-affiliated 5493 :mode nil :granularity nil :parent #187) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #203))) (paragraph (:begin 5600 :end 5763 :contents-begin 5600 :contents-end 5762 :post-blank 1 :post-affiliated 5600 :mode nil :granularity nil :parent #187) #("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 #204))) (paragraph (:begin 5763 :end 5895 :contents-begin 5763 :contents-end 5895 :post-blank 0 :post-affiliated 5763 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 5814 :end 5821 :use-brackets-p nil :contents-begin 5815 :contents-end 5821 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 5821 :end 5823 :use-brackets-p nil :contents-begin 5822 :contents-end 5823 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 5862 :end 5875 :use-brackets-p nil :contents-begin 5863 :contents-end 5874 :post-blank 1 :parent #205) #("settings.py" 0 11 (:parent #212))) #("to match your path.\n" 0 20 (:parent #205)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5896 :end 6060 :pre-blank 1 :contents-begin 5920 :contents-end 6059 :robust-begin 5922 :robust-end 6057 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5896 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 5920 :end 6060 :contents-begin 5920 :contents-end 6059 :robust-begin 5920 :robust-end 6057 :post-blank 1 :post-affiliated 5920 :mode section :granularity nil :parent #181) (paragraph (:begin 5920 :end 5981 :contents-begin 5920 :contents-end 5980 :post-blank 1 :post-affiliated 5920 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 5981 :end 6059 :contents-begin 6011 :contents-end 6059 :post-blank 0 :post-affiliated 6011 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #184) (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 6011 :end 6058 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #("\n" 0 1 (:parent #188))))) (headline (:raw-value "Working with the GN2 source code" :begin 6060 :end 6122 :pre-blank 1 :contents-begin 6096 :contents-end 6121 :robust-begin 6098 :robust-end 6119 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6060 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 6096 :end 6122 :contents-begin 6096 :contents-end 6121 :robust-begin 6096 :robust-end 6119 :post-blank 1 :post-affiliated 6096 :mode section :granularity nil :parent #182) (paragraph (:begin 6096 :end 6121 :contents-begin 6096 :contents-end 6121 :post-blank 0 :post-affiliated 6096 :mode planning :granularity nil :parent #185) #("See " 0 4 (:parent #188)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6100 :end 6119 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Trouble shooting" :begin 6122 :end 8347 :pre-blank 1 :contents-begin 6142 :contents-end 8346 :robust-begin 6144 :robust-end 8344 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6122 :title (#("Trouble shooting" 0 16 (:parent #183))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6142 :end 6676 :pre-blank 1 :contents-begin 6182 :contents-end 6676 :robust-begin 6184 :robust-end 6674 :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 6142 :title (#("ImportError: No module named jinja2" 0 35 (:parent #186))) :mode section :granularity nil :parent #183) (section (:begin 6182 :end 6676 :contents-begin 6182 :contents-end 6676 :robust-begin 6182 :robust-end 6674 :post-blank 0 :post-affiliated 6182 :mode section :granularity nil :parent #186) (paragraph (:begin 6182 :end 6417 :contents-begin 6182 :contents-end 6416 :post-blank 1 :post-affiliated 6182 :mode planning :granularity nil :parent #189) #("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 #192)) (subscript (:begin 6349 :end 6355 :use-brackets-p nil :contents-begin 6350 :contents-end 6354 :post-blank 1 :parent #192) #("PATH" 0 4 (:parent #196))) #("and R" 0 5 (:parent #192)) (subscript (:begin 6360 :end 6365 :use-brackets-p nil :contents-begin 6361 :contents-end 6365 :post-blank 0 :parent #192) #("LIBS" 0 4 (:parent #198))) (subscript (:begin 6365 :end 6371 :use-brackets-p nil :contents-begin 6366 :contents-end 6370 :post-blank 1 :parent #192) #("SITE" 0 4 (:parent #199))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #192))) (fixed-width (:begin 6417 :end 6448 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6417 :mode nil :granularity nil :parent #189)) (paragraph (:begin 6448 :end 6464 :contents-begin 6448 :contents-end 6463 :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #189) #("On one system:\n" 0 15 (:parent #194))) (fixed-width (:begin 6464 :end 6652 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6464 :mode nil :granularity nil :parent #189)) (paragraph (:begin 6652 :end 6676 :contents-begin 6652 :contents-end 6676 :post-blank 0 :post-affiliated 6652 :mode nil :granularity nil :parent #189) #("and perhaps a few more.\n" 0 24 (:parent #196))))) (headline (:raw-value "ERROR: can not find directory $HOME/gn2_data" :begin 6676 :end 6947 :pre-blank 1 :contents-begin 6725 :contents-end 6946 :robust-begin 6727 :robust-end 6944 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6676 :title (#("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #187)) (subscript (:begin 6718 :end 6723 :use-brackets-p nil :contents-begin 6719 :contents-end 6723 :post-blank 0 :parent #187) #("data" 0 4 (:parent #229)))) :mode nil :granularity nil :parent #183) (section (:begin 6725 :end 6947 :contents-begin 6725 :contents-end 6946 :robust-begin 6725 :robust-end 6944 :post-blank 1 :post-affiliated 6725 :mode section :granularity nil :parent #187) (paragraph (:begin 6725 :end 6946 :contents-begin 6725 :contents-end 6946 :post-blank 0 :post-affiliated 6725 :mode planning :granularity nil :parent #190) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #193)) (subscript (:begin 6774 :end 6779 :use-brackets-p nil :contents-begin 6775 :contents-end 6779 :post-blank 0 :parent #193) #("data" 0 4 (:parent #197))) #(". 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 #193)) (subscript (:begin 6903 :end 6916 :use-brackets-p nil :contents-begin 6904 :contents-end 6915 :post-blank 1 :parent #193) #("settings.py" 0 11 (:parent #199))) #("(see above in\nthis document).\n" 0 30 (:parent #193))))) (headline (:raw-value "Can't run a module" :begin 6947 :end 7181 :pre-blank 1 :contents-begin 6970 :contents-end 7181 :robust-begin 6972 :robust-end 7179 :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 6947 :title (#("Can't run a module" 0 18 (:parent #188))) :mode nil :granularity nil :parent #183) (section (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :robust-begin 6970 :robust-end 7179 :post-blank 0 :post-affiliated 6970 :mode section :granularity nil :parent #188) (paragraph (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :post-blank 0 :post-affiliated 6970 :mode planning :granularity nil :parent #191) #("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 #194))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7181 :end 7682 :pre-blank 1 :contents-begin 7213 :contents-end 7681 :robust-begin 7215 :robust-end 7679 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7181 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #189))) :mode nil :granularity nil :parent #183) (section (:begin 7213 :end 7682 :contents-begin 7213 :contents-end 7681 :robust-begin 7213 :robust-end 7679 :post-blank 1 :post-affiliated 7213 :mode section :granularity nil :parent #189) (paragraph (:begin 7213 :end 7225 :contents-begin 7213 :contents-end 7224 :post-blank 1 :post-affiliated 7213 :mode planning :granularity nil :parent #192) #("This error\n" 0 11 (:parent #195))) (fixed-width (:begin 7225 :end 7305 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7225 :mode nil :granularity nil :parent #192)) (paragraph (:begin 7305 :end 7436 :contents-begin 7305 :contents-end 7435 :post-blank 1 :post-affiliated 7305 :mode nil :granularity nil :parent #192) #("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 #197))) (paragraph (:begin 7436 :end 7681 :contents-begin 7436 :contents-end 7681 :post-blank 0 :post-affiliated 7436 :mode nil :granularity nil :parent #192) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #198)) (subscript (:begin 7499 :end 7504 :use-brackets-p nil :contents-begin 7500 :contents-end 7504 :post-blank 0 :parent #198) #("LIBS" 0 4 (:parent #202))) (subscript (:begin 7504 :end 7509 :use-brackets-p nil :contents-begin 7505 :contents-end 7509 :post-blank 0 :parent #198) #("SITE" 0 4 (:parent #203))) #(". 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 #198))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7682 :end 8347 :pre-blank 1 :contents-begin 7734 :contents-end 8346 :robust-begin 7736 :robust-end 8344 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7682 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #190))) :mode nil :granularity nil :parent #183) (section (:begin 7734 :end 8347 :contents-begin 7734 :contents-end 8346 :robust-begin 7734 :robust-end 8344 :post-blank 1 :post-affiliated 7734 :mode section :granularity nil :parent #190) (paragraph (:begin 7734 :end 7755 :contents-begin 7734 :contents-end 7754 :post-blank 1 :post-affiliated 7734 :mode planning :granularity nil :parent #193) #("The following error\n" 0 20 (:parent #196))) (fixed-width (:begin 7755 :end 7950 :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 7755 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7950 :end 8108 :contents-begin 7950 :contents-end 8107 :post-blank 1 :post-affiliated 7950 :mode nil :granularity nil :parent #193) #("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 #198))) (fixed-width (:begin 8108 :end 8130 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8108 :mode nil :granularity nil :parent #193)) (paragraph (:begin 8130 :end 8187 :contents-begin 8130 :contents-end 8186 :post-blank 1 :post-affiliated 8130 :mode nil :granularity nil :parent #193) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #200))) (fixed-width (:begin 8187 :end 8209 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8187 :mode nil :granularity nil :parent #193)) (paragraph (:begin 8209 :end 8280 :contents-begin 8209 :contents-end 8279 :post-blank 1 :post-affiliated 8209 :mode nil :granularity nil :parent #193) #("if that works run genenetwork after setting SQL" 0 47 (:parent #202)) (subscript (:begin 8256 :end 8261 :use-brackets-p nil :contents-begin 8257 :contents-end 8260 :post-blank 1 :parent #202) #("URI" 0 3 (:parent #206))) #("to something like\n" 0 18 (:parent #202))) (fixed-width (:begin 8280 :end 8346 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8280 :mode nil :granularity nil :parent #193))))) (headline (:raw-value "Read more" :begin 8347 :end 8497 :pre-blank 1 :contents-begin 8360 :contents-end 8496 :robust-begin 8362 :robust-end 8494 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8347 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 8360 :end 8497 :contents-begin 8360 :contents-end 8496 :robust-begin 8360 :robust-end 8494 :post-blank 1 :post-affiliated 8360 :mode section :granularity nil :parent #184) (paragraph (:begin 8360 :end 8496 :contents-begin 8360 :contents-end 8496 :post-blank 0 :post-affiliated 8360 :mode planning :granularity nil :parent #187) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #190)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 8415 :end 8435 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #190))))) (headline (:raw-value "IRC session" :begin 8497 :end 15385 :pre-blank 1 :contents-begin 8512 :contents-end 15385 :robust-begin 8514 :robust-end 15383 :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 8497 :title (#("IRC session" 0 11 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 8512 :end 15385 :contents-begin 8512 :contents-end 15385 :robust-begin 8512 :robust-end 15383 :post-blank 0 :post-affiliated 8512 :mode section :granularity nil :parent #185) (paragraph (:begin 8512 :end 8621 :contents-begin 8512 :contents-end 8620 :post-blank 1 :post-affiliated 8512 :mode planning :granularity nil :parent #188) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #191))) (paragraph (:begin 8621 :end 9182 :contents-begin 8621 :contents-end 9181 :post-blank 1 :post-affiliated 8621 :mode nil :granularity nil :parent #188) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 8628 :end 8632 :use-brackets-p nil :contents-begin 8629 :contents-end 8632 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #192))) (paragraph (:begin 9182 :end 9272 :contents-begin 9182 :contents-end 9271 :post-blank 1 :post-affiliated 9182 :mode nil :granularity nil :parent #188) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 9272 :end 9417 :contents-begin 9272 :contents-end 9416 :post-blank 1 :post-affiliated 9272 :mode nil :granularity nil :parent #188) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 9302 :end 9310 :use-brackets-p nil :contents-begin 9303 :contents-end 9310 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 9310 :end 9315 :use-brackets-p nil :contents-begin 9311 :contents-end 9315 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 9417 :end 9713 :contents-begin 9417 :contents-end 9712 :post-blank 1 :post-affiliated 9417 :mode nil :granularity nil :parent #188) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 9713 :end 10906 :contents-begin 9713 :contents-end 10905 :post-blank 1 :post-affiliated 9713 :mode nil :granularity nil :parent #188) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #196)) (subscript (:begin 10466 :end 10474 :use-brackets-p nil :contents-begin 10467 :contents-end 10474 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 10474 :end 10479 :use-brackets-p nil :contents-begin 10475 :contents-end 10479 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 10906 :end 11110 :contents-begin 10906 :contents-end 11109 :post-blank 1 :post-affiliated 10906 :mode nil :granularity nil :parent #188) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 11110 :end 15385 :contents-begin 11110 :contents-end 15385 :post-blank 0 :post-affiliated 11110 :mode nil :granularity nil :parent #188) #(" which should have the same HASH values " 0 48 (:parent #198)) (italic (:begin 11158 :end 12067 :post-blank 0 :contents-begin 11159 :contents-end 12066 :parent #198) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #202))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #198)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12867 :end 12932 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13180 :end 13213 :contents-begin nil :contents-end nil :post-blank 1 :parent #198)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #198)) (subscript (:begin 13437 :end 13445 :use-brackets-p nil :contents-begin 13438 :contents-end 13445 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #208))) (subscript (:begin 13445 :end 13450 :use-brackets-p nil :contents-begin 13446 :contents-end 13450 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #209))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #198)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13566 :end 13593 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #198)) (subscript (:begin 14163 :end 14171 :use-brackets-p nil :contents-begin 14164 :contents-end 14171 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #213))) (subscript (:begin 14171 :end 14176 :use-brackets-p nil :contents-begin 14172 :contents-end 14176 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #214))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #198)) (subscript (:begin 14835 :end 14843 :use-brackets-p nil :contents-begin 14836 :contents-end 14843 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #216))) (subscript (:begin 14843 :end 14848 :use-brackets-p nil :contents-begin 14844 :contents-end 14848 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #217))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #198)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14962 :end 14994 :contents-begin nil :contents-end nil :post-blank 0 :parent #198)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n" 0 391 (:parent #198))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 268 :contents-begin 159 :contents-end 268 :checkbox nil :counter nil :structure ((121 1 "- " nil nil nil 156) (156 1 "- " nil nil nil 268) (181 3 "- " nil nil nil 208) (208 3 "- " nil nil nil 233) (233 3 "- " nil nil nil 268) (268 1 "- " nil nil nil 301) (301 1 "- " nil nil nil 488) (344 3 "- " nil nil nil 411) (411 3 "- " nil nil nil 488) (488 1 "- " nil nil nil 539) (539 1 "- " nil nil nil 614) (614 1 "- " nil nil nil 1056) (657 3 "- " nil nil nil 739) (739 3 "- " nil nil nil 837) (837 3 "- " nil nil nil 885) (885 3 "- " nil nil nil 950) (950 3 "- " nil nil nil 1056) (1056 1 "- " nil nil nil 1085) (1085 1 "- " nil nil nil 1118)) :pre-blank 0 :post-blank 0 :post-affiliated 156 :tag nil :mode item :granularity nil :parent #78) (paragraph (:begin 159 :end 181 :contents-begin 159 :contents-end 181 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #349)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1364 :end 1438 :contents-begin 1426 :contents-end 1436 :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 1521 :end 1871 :contents-begin 1521 :contents-end 1870 :post-blank 1 :post-affiliated 1521 :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 1739 :end 1815 :contents-begin 1793 :contents-end 1812 :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 1819 :end 1868 :contents-begin 1858 :contents-end 1866 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 1871 :end 2006 :contents-begin 1871 :contents-end 2006 :post-blank 0 :post-affiliated 1871 :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 1957 :end 2004 :contents-begin 1982 :contents-end 2002 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2007 :end 3390 :pre-blank 1 :contents-begin 2018 :contents-end 3389 :robust-begin 2020 :robust-end 3387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2007 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2018 :end 2382 :contents-begin 2018 :contents-end 2381 :robust-begin 2018 :robust-end 2379 :post-blank 1 :post-affiliated 2018 :mode section :granularity nil :parent #344) (paragraph (:begin 2018 :end 2381 :contents-begin 2018 :contents-end 2381 :post-blank 0 :post-affiliated 2018 :mode planning :granularity nil :parent #347) #("The quickest way to install GN2 is by using a binary installation\n(tarball or Docker image). These installations are bundled by GNU\nGuix and include all dependencies. You can install GeneNetwork on most\nLinux distributions, including Debian, Ubuntu, Fedora and CentOS,\nprovided you have administrator privileges (root). The alternative is\na Docker installation.\n" 0 363 (:parent #350)))) (headline (:raw-value "Tarball" :begin 2382 :end 3035 :pre-blank 1 :contents-begin 2394 :contents-end 3034 :robust-begin 2396 :robust-end 3032 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2382 :title (#("Tarball" 0 7 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2394 :end 3035 :contents-begin 2394 :contents-end 3034 :robust-begin 2394 :robust-end 3032 :post-blank 1 :post-affiliated 2394 :mode section :granularity nil :parent #348) (paragraph (:begin 2394 :end 2541 :contents-begin 2394 :contents-end 2540 :post-blank 1 :post-affiliated 2394 :mode planning :granularity nil :parent #351) #("Download the ~800Mb tarball from\n" 0 33 (:parent #354)) (link (:type "http" :path "//files.genenetwork.org/software/binary_tarball/" :format bracket :raw-link "http://files.genenetwork.org/software/binary_tarball/" :application nil :search-option nil :begin 2427 :end 2484 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(". Validate the checksum and\nunpack to root, for example\n" 0 56 (:parent #354))) (fixed-width (:begin 2541 :end 2643 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2541 :mode nil :granularity nil :parent #351)) (paragraph (:begin 2643 :end 2691 :contents-begin 2643 :contents-end 2690 :post-blank 1 :post-affiliated 2643 :mode nil :granularity nil :parent #351) #("Now you shoud be able to start the server with\n" 0 47 (:parent #356))) (fixed-width (:begin 2691 :end 2729 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2691 :mode nil :granularity nil :parent #351)) (paragraph (:begin 2729 :end 2856 :contents-begin 2729 :contents-end 2855 :post-blank 1 :post-affiliated 2729 :mode nil :granularity nil :parent #351) #("When the server stops with a MySQL error " 0 41 (:parent #358)) (link (:type "custom-id" :path "run-mysql-server" :format bracket :raw-link "#run-mysql-server" :application nil :search-option nil :begin 2770 :end 2809 :contents-begin 2791 :contents-end 2807 :post-blank 0 :parent #358) #("Run MySQL server" 0 16 (:parent #362))) #("\nand set SQL" 0 12 (:parent #358)) (subscript (:begin 2821 :end 2826 :use-brackets-p nil :contents-begin 2822 :contents-end 2825 :post-blank 1 :parent #358) #("URI" 0 3 (:parent #364))) #("to point at it. For example:\n" 0 29 (:parent #358))) (fixed-width (:begin 2856 :end 2923 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 2856 :mode nil :granularity nil :parent #351)) (paragraph (:begin 2923 :end 3034 :contents-begin 2923 :contents-end 3034 :post-blank 0 :post-affiliated 2923 :mode nil :granularity nil :parent #351) #("See also " 0 9 (:parent #360)) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 2932 :end 3032 :contents-begin 2983 :contents-end 3030 :post-blank 0 :parent #360) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #364))) #(".\n" 0 2 (:parent #360))))) (headline (:raw-value "Docker" :begin 3035 :end 3244 :pre-blank 1 :contents-begin 3046 :contents-end 3243 :robust-begin 3048 :robust-end 3241 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3035 :title (#("Docker" 0 6 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 3046 :end 3244 :contents-begin 3046 :contents-end 3243 :robust-begin 3046 :robust-end 3241 :post-blank 1 :post-affiliated 3046 :mode section :granularity nil :parent #349) (paragraph (:begin 3046 :end 3243 :contents-begin 3046 :contents-end 3243 :post-blank 0 :post-affiliated 3046 :mode planning :granularity nil :parent #352) #("Docker images are also available through\n" 0 41 (:parent #355)) (link (:type "http" :path "//files.genenetwork.org/software/" :format bracket :raw-link "http://files.genenetwork.org/software/" :application nil :search-option nil :begin 3087 :end 3129 :contents-begin nil :contents-end nil :post-blank 0 :parent #355)) #(". Validate the checksum and run\nwith " 0 37 (:parent #355)) (link (:type "https" :path "//docs.docker.com/engine/reference/commandline/load/" :format bracket :raw-link "https://docs.docker.com/engine/reference/commandline/load/" :application nil :search-option nil :begin 3166 :end 3241 :contents-begin 3228 :contents-end 3239 :post-blank 0 :parent #355) #("Docker load" 0 11 (:parent #361))) #(".\n" 0 2 (:parent #355))))) (headline (:raw-value "With source" :begin 3244 :end 3390 :pre-blank 1 :contents-begin 3260 :contents-end 3389 :robust-begin 3262 :robust-end 3387 :level 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 (#("With source" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 3260 :end 3390 :contents-begin 3260 :contents-end 3389 :robust-begin 3260 :robust-end 3387 :post-blank 1 :post-affiliated 3260 :mode section :granularity nil :parent #350) (paragraph (:begin 3260 :end 3389 :contents-begin 3260 :contents-end 3389 :post-blank 0 :post-affiliated 3260 :mode planning :granularity nil :parent #353) #("For more elaborate installation instructions on deploying GeneNetwork from\nsource see " 0 86 (:parent #356)) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 3346 :end 3387 :contents-begin 3368 :contents-end 3385 :post-blank 0 :parent #356) #("Source deployment" 0 17 (:parent #360))) #(".\n" 0 2 (:parent #356)))))) (headline (:raw-value "Running GN2" :begin 3390 :end 3871 :pre-blank 1 :contents-begin 3405 :contents-end 3870 :robust-begin 3407 :robust-end 3868 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3390 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 3405 :end 3871 :contents-begin 3405 :contents-end 3870 :robust-begin 3405 :robust-end 3868 :post-blank 1 :post-affiliated 3405 :mode section :granularity nil :parent #345) (paragraph (:begin 3405 :end 3600 :contents-begin 3405 :contents-end 3599 :post-blank 1 :post-affiliated 3405 :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 3458 :end 3509 :contents-begin 3488 :contents-end 3507 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 3495 :end 3507 :use-brackets-p nil :contents-begin 3496 :contents-end 3507 :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 3600 :end 3630 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3600 :mode nil :granularity nil :parent #348)) (paragraph (:begin 3630 :end 3708 :contents-begin 3630 :contents-end 3707 :post-blank 1 :post-affiliated 3630 :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 3708 :end 3791 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3708 :mode nil :granularity nil :parent #348)) (paragraph (:begin 3791 :end 3870 :contents-begin 3791 :contents-end 3870 :post-blank 0 :post-affiliated 3791 :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 MySQL server" :begin 3871 :end 5896 :pre-blank 0 :contents-begin 3890 :contents-end 5895 :robust-begin 3892 :robust-end 5893 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3871 :title (#("Run MySQL server" 0 16 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 3890 :end 4364 :pre-blank 1 :contents-begin 3922 :contents-end 4363 :robust-begin 3924 :robust-end 4361 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3890 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 3922 :end 4364 :contents-begin 3922 :contents-end 4363 :robust-begin 3922 :robust-end 4361 :post-blank 1 :post-affiliated 3922 :mode section :granularity nil :parent #349) (paragraph (:begin 3922 :end 4057 :contents-begin 3922 :contents-end 4056 :post-blank 1 :post-affiliated 3922 :mode planning :granularity nil :parent #352) #("These are the steps you can take to install a fresh installation of\nmysql (which comes as part of the GNU Guix genenetwork2 install).\n" 0 134 (:parent #355))) (paragraph (:begin 4057 :end 4084 :contents-begin 4057 :contents-end 4083 :post-blank 1 :post-affiliated 4057 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #356))) (fixed-width (:begin 4084 :end 4332 :value " adduser mysql && addgroup mysql\n mysqld --datadir=/var/mysql --initialize-insecure\n mkdir -p /var/run/mysqld\n chown mysql.mysql ~/mysql /var/run/mysqld\n su mysql -c mysqld --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" :post-blank 2 :post-affiliated 4084 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4332 :end 4363 :contents-begin 4332 :contents-end 4363 :post-blank 0 :post-affiliated 4332 :mode nil :granularity nil :parent #352) #("/etc/my.cnf\n[mysqld]\nuser=root\n" 0 31 (:parent #358))))) (headline (:raw-value "Load the small database in MySQL" :begin 4364 :end 5896 :pre-blank 1 :contents-begin 4401 :contents-end 5895 :robust-begin 4403 :robust-end 5893 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4364 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 4401 :end 5896 :contents-begin 4401 :contents-end 5895 :robust-begin 4401 :robust-end 5893 :post-blank 1 :post-affiliated 4401 :mode section :granularity nil :parent #350) (paragraph (:begin 4401 :end 4708 :contents-begin 4401 :contents-end 4707 :post-blank 1 :post-affiliated 4401 :mode planning :granularity nil :parent #353) #("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 #356)) (subscript (:begin 4564 :end 4571 :use-brackets-p nil :contents-begin 4565 :contents-end 4571 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 4571 :end 4573 :use-brackets-p nil :contents-begin 4572 :contents-end 4573 :post-blank 0 :parent #356) #("s" 0 1 (:parent #361))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #356)) (subscript (:begin 4649 :end 4656 :use-brackets-p nil :contents-begin 4650 :contents-end 4656 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 4656 :end 4662 :use-brackets-p nil :contents-begin 4657 :contents-end 4662 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 4708 :end 4736 :contents-begin 4708 :contents-end 4735 :post-blank 1 :post-affiliated 4708 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 4736 :end 4784 :contents-begin 4736 :contents-end 4783 :post-blank 1 :post-affiliated 4736 :mode nil :granularity nil :parent #353) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4736 :end 4782 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 4784 :end 4843 :contents-begin 4784 :contents-end 4842 :post-blank 1 :post-affiliated 4784 :mode nil :granularity nil :parent #353) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4784 :end 4841 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 4843 :end 4862 :contents-begin 4843 :contents-end 4861 :post-blank 1 :post-affiliated 4843 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 4862 :end 4933 :contents-begin 4862 :contents-end 4932 :post-blank 1 :post-affiliated 4862 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 4933 :end 5034 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4933 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5034 :end 5081 :contents-begin 5034 :contents-end 5080 :post-blank 1 :post-affiliated 5034 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5081 :end 5098 :value "myslq -u root" :post-blank 2 :post-affiliated 5081 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5098 :end 5103 :contents-begin 5098 :contents-end 5102 :post-blank 1 :post-affiliated 5098 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 5103 :end 5329 :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 5103 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5329 :end 5394 :contents-begin 5329 :contents-end 5393 :post-blank 1 :post-affiliated 5329 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 5394 :end 5493 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5394 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5493 :end 5600 :contents-begin 5493 :contents-end 5599 :post-blank 1 :post-affiliated 5493 :mode nil :granularity nil :parent #353) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #369))) (paragraph (:begin 5600 :end 5763 :contents-begin 5600 :contents-end 5762 :post-blank 1 :post-affiliated 5600 :mode nil :granularity nil :parent #353) #("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 #370))) (paragraph (:begin 5763 :end 5895 :contents-begin 5763 :contents-end 5895 :post-blank 0 :post-affiliated 5763 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 5814 :end 5821 :use-brackets-p nil :contents-begin 5815 :contents-end 5821 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 5821 :end 5823 :use-brackets-p nil :contents-begin 5822 :contents-end 5823 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 5862 :end 5875 :use-brackets-p nil :contents-begin 5863 :contents-end 5874 :post-blank 1 :parent #371) #("settings.py" 0 11 (:parent #378))) #("to match your path.\n" 0 20 (:parent #371)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5896 :end 6060 :pre-blank 1 :contents-begin 5920 :contents-end 6059 :robust-begin 5922 :robust-end 6057 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5896 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 5920 :end 6060 :contents-begin 5920 :contents-end 6059 :robust-begin 5920 :robust-end 6057 :post-blank 1 :post-affiliated 5920 :mode section :granularity nil :parent #347) (paragraph (:begin 5920 :end 5981 :contents-begin 5920 :contents-end 5980 :post-blank 1 :post-affiliated 5920 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 5981 :end 6059 :contents-begin 6011 :contents-end 6059 :post-blank 0 :post-affiliated 6011 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #350) (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 6011 :end 6058 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #("\n" 0 1 (:parent #354))))) (headline (:raw-value "Working with the GN2 source code" :begin 6060 :end 6122 :pre-blank 1 :contents-begin 6096 :contents-end 6121 :robust-begin 6098 :robust-end 6119 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6060 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 6096 :end 6122 :contents-begin 6096 :contents-end 6121 :robust-begin 6096 :robust-end 6119 :post-blank 1 :post-affiliated 6096 :mode section :granularity nil :parent #348) (paragraph (:begin 6096 :end 6121 :contents-begin 6096 :contents-end 6121 :post-blank 0 :post-affiliated 6096 :mode planning :granularity nil :parent #351) #("See " 0 4 (:parent #354)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6100 :end 6119 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Trouble shooting" :begin 6122 :end 8347 :pre-blank 1 :contents-begin 6142 :contents-end 8346 :robust-begin 6144 :robust-end 8344 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6122 :title (#("Trouble shooting" 0 16 (:parent #349))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 6142 :end 6676 :pre-blank 1 :contents-begin 6182 :contents-end 6676 :robust-begin 6184 :robust-end 6674 :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 6142 :title (#("ImportError: No module named jinja2" 0 35 (:parent #352))) :mode section :granularity nil :parent #349) (section (:begin 6182 :end 6676 :contents-begin 6182 :contents-end 6676 :robust-begin 6182 :robust-end 6674 :post-blank 0 :post-affiliated 6182 :mode section :granularity nil :parent #352) (paragraph (:begin 6182 :end 6417 :contents-begin 6182 :contents-end 6416 :post-blank 1 :post-affiliated 6182 :mode planning :granularity nil :parent #355) #("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 #358)) (subscript (:begin 6349 :end 6355 :use-brackets-p nil :contents-begin 6350 :contents-end 6354 :post-blank 1 :parent #358) #("PATH" 0 4 (:parent #362))) #("and R" 0 5 (:parent #358)) (subscript (:begin 6360 :end 6365 :use-brackets-p nil :contents-begin 6361 :contents-end 6365 :post-blank 0 :parent #358) #("LIBS" 0 4 (:parent #364))) (subscript (:begin 6365 :end 6371 :use-brackets-p nil :contents-begin 6366 :contents-end 6370 :post-blank 1 :parent #358) #("SITE" 0 4 (:parent #365))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #358))) (fixed-width (:begin 6417 :end 6448 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6417 :mode nil :granularity nil :parent #355)) (paragraph (:begin 6448 :end 6464 :contents-begin 6448 :contents-end 6463 :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #355) #("On one system:\n" 0 15 (:parent #360))) (fixed-width (:begin 6464 :end 6652 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6464 :mode nil :granularity nil :parent #355)) (paragraph (:begin 6652 :end 6676 :contents-begin 6652 :contents-end 6676 :post-blank 0 :post-affiliated 6652 :mode nil :granularity nil :parent #355) #("and perhaps a few more.\n" 0 24 (:parent #362))))) (headline (:raw-value "ERROR: can not find directory $HOME/gn2_data" :begin 6676 :end 6947 :pre-blank 1 :contents-begin 6725 :contents-end 6946 :robust-begin 6727 :robust-end 6944 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6676 :title (#("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #353)) (subscript (:begin 6718 :end 6723 :use-brackets-p nil :contents-begin 6719 :contents-end 6723 :post-blank 0 :parent #353) #("data" 0 4 (:parent #395)))) :mode nil :granularity nil :parent #349) (section (:begin 6725 :end 6947 :contents-begin 6725 :contents-end 6946 :robust-begin 6725 :robust-end 6944 :post-blank 1 :post-affiliated 6725 :mode section :granularity nil :parent #353) (paragraph (:begin 6725 :end 6946 :contents-begin 6725 :contents-end 6946 :post-blank 0 :post-affiliated 6725 :mode planning :granularity nil :parent #356) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #359)) (subscript (:begin 6774 :end 6779 :use-brackets-p nil :contents-begin 6775 :contents-end 6779 :post-blank 0 :parent #359) #("data" 0 4 (:parent #363))) #(". 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 #359)) (subscript (:begin 6903 :end 6916 :use-brackets-p nil :contents-begin 6904 :contents-end 6915 :post-blank 1 :parent #359) #("settings.py" 0 11 (:parent #365))) #("(see above in\nthis document).\n" 0 30 (:parent #359))))) (headline (:raw-value "Can't run a module" :begin 6947 :end 7181 :pre-blank 1 :contents-begin 6970 :contents-end 7181 :robust-begin 6972 :robust-end 7179 :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 6947 :title (#("Can't run a module" 0 18 (:parent #354))) :mode nil :granularity nil :parent #349) (section (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :robust-begin 6970 :robust-end 7179 :post-blank 0 :post-affiliated 6970 :mode section :granularity nil :parent #354) (paragraph (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :post-blank 0 :post-affiliated 6970 :mode planning :granularity nil :parent #357) #("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 #360))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7181 :end 7682 :pre-blank 1 :contents-begin 7213 :contents-end 7681 :robust-begin 7215 :robust-end 7679 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7181 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #355))) :mode nil :granularity nil :parent #349) (section (:begin 7213 :end 7682 :contents-begin 7213 :contents-end 7681 :robust-begin 7213 :robust-end 7679 :post-blank 1 :post-affiliated 7213 :mode section :granularity nil :parent #355) (paragraph (:begin 7213 :end 7225 :contents-begin 7213 :contents-end 7224 :post-blank 1 :post-affiliated 7213 :mode planning :granularity nil :parent #358) #("This error\n" 0 11 (:parent #361))) (fixed-width (:begin 7225 :end 7305 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7225 :mode nil :granularity nil :parent #358)) (paragraph (:begin 7305 :end 7436 :contents-begin 7305 :contents-end 7435 :post-blank 1 :post-affiliated 7305 :mode nil :granularity nil :parent #358) #("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 #363))) (paragraph (:begin 7436 :end 7681 :contents-begin 7436 :contents-end 7681 :post-blank 0 :post-affiliated 7436 :mode nil :granularity nil :parent #358) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #364)) (subscript (:begin 7499 :end 7504 :use-brackets-p nil :contents-begin 7500 :contents-end 7504 :post-blank 0 :parent #364) #("LIBS" 0 4 (:parent #368))) (subscript (:begin 7504 :end 7509 :use-brackets-p nil :contents-begin 7505 :contents-end 7509 :post-blank 0 :parent #364) #("SITE" 0 4 (:parent #369))) #(". 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 #364))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7682 :end 8347 :pre-blank 1 :contents-begin 7734 :contents-end 8346 :robust-begin 7736 :robust-end 8344 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7682 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #356))) :mode nil :granularity nil :parent #349) (section (:begin 7734 :end 8347 :contents-begin 7734 :contents-end 8346 :robust-begin 7734 :robust-end 8344 :post-blank 1 :post-affiliated 7734 :mode section :granularity nil :parent #356) (paragraph (:begin 7734 :end 7755 :contents-begin 7734 :contents-end 7754 :post-blank 1 :post-affiliated 7734 :mode planning :granularity nil :parent #359) #("The following error\n" 0 20 (:parent #362))) (fixed-width (:begin 7755 :end 7950 :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 7755 :mode nil :granularity nil :parent #359)) (paragraph (:begin 7950 :end 8108 :contents-begin 7950 :contents-end 8107 :post-blank 1 :post-affiliated 7950 :mode nil :granularity nil :parent #359) #("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 #364))) (fixed-width (:begin 8108 :end 8130 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8108 :mode nil :granularity nil :parent #359)) (paragraph (:begin 8130 :end 8187 :contents-begin 8130 :contents-end 8186 :post-blank 1 :post-affiliated 8130 :mode nil :granularity nil :parent #359) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #366))) (fixed-width (:begin 8187 :end 8209 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8187 :mode nil :granularity nil :parent #359)) (paragraph (:begin 8209 :end 8280 :contents-begin 8209 :contents-end 8279 :post-blank 1 :post-affiliated 8209 :mode nil :granularity nil :parent #359) #("if that works run genenetwork after setting SQL" 0 47 (:parent #368)) (subscript (:begin 8256 :end 8261 :use-brackets-p nil :contents-begin 8257 :contents-end 8260 :post-blank 1 :parent #368) #("URI" 0 3 (:parent #372))) #("to something like\n" 0 18 (:parent #368))) (fixed-width (:begin 8280 :end 8346 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8280 :mode nil :granularity nil :parent #359))))) (headline (:raw-value "Read more" :begin 8347 :end 8497 :pre-blank 1 :contents-begin 8360 :contents-end 8496 :robust-begin 8362 :robust-end 8494 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8347 :title (#("Read more" 0 9 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 8360 :end 8497 :contents-begin 8360 :contents-end 8496 :robust-begin 8360 :robust-end 8494 :post-blank 1 :post-affiliated 8360 :mode section :granularity nil :parent #350) (paragraph (:begin 8360 :end 8496 :contents-begin 8360 :contents-end 8496 :post-blank 0 :post-affiliated 8360 :mode planning :granularity nil :parent #353) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #356)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 8415 :end 8435 :contents-begin nil :contents-end nil :post-blank 0 :parent #356)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #356))))) (headline (:raw-value "IRC session" :begin 8497 :end 15385 :pre-blank 1 :contents-begin 8512 :contents-end 15385 :robust-begin 8514 :robust-end 15383 :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 8497 :title (#("IRC session" 0 11 (:parent #351))) :mode nil :granularity nil :parent #338) (section (:begin 8512 :end 15385 :contents-begin 8512 :contents-end 15385 :robust-begin 8512 :robust-end 15383 :post-blank 0 :post-affiliated 8512 :mode section :granularity nil :parent #351) (paragraph (:begin 8512 :end 8621 :contents-begin 8512 :contents-end 8620 :post-blank 1 :post-affiliated 8512 :mode planning :granularity nil :parent #354) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #357))) (paragraph (:begin 8621 :end 9182 :contents-begin 8621 :contents-end 9181 :post-blank 1 :post-affiliated 8621 :mode nil :granularity nil :parent #354) #("#+begin" 0 7 (:parent #358)) (subscript (:begin 8628 :end 8632 :use-brackets-p nil :contents-begin 8629 :contents-end 8632 :post-blank 0 :parent #358) #("src" 0 3 (:parent #362))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #358))) (paragraph (:begin 9182 :end 9272 :contents-begin 9182 :contents-end 9271 :post-blank 1 :post-affiliated 9182 :mode nil :granularity nil :parent #354) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #359))) (paragraph (:begin 9272 :end 9417 :contents-begin 9272 :contents-end 9416 :post-blank 1 :post-affiliated 9272 :mode nil :granularity nil :parent #354) #(" yes\n env GUIX" 0 30 (:parent #360)) (subscript (:begin 9302 :end 9310 :use-brackets-p nil :contents-begin 9303 :contents-end 9310 :post-blank 0 :parent #360) #("PACKAGE" 0 7 (:parent #364))) (subscript (:begin 9310 :end 9315 :use-brackets-p nil :contents-begin 9311 :contents-end 9315 :post-blank 0 :parent #360) #("PATH" 0 4 (:parent #365))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #360))) (paragraph (:begin 9417 :end 9713 :contents-begin 9417 :contents-end 9712 :post-blank 1 :post-affiliated 9417 :mode nil :granularity nil :parent #354) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #361))) (paragraph (:begin 9713 :end 10906 :contents-begin 9713 :contents-end 10905 :post-blank 1 :post-affiliated 9713 :mode nil :granularity nil :parent #354) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #362)) (subscript (:begin 10466 :end 10474 :use-brackets-p nil :contents-begin 10467 :contents-end 10474 :post-blank 0 :parent #362) #("PACKAGE" 0 7 (:parent #366))) (subscript (:begin 10474 :end 10479 :use-brackets-p nil :contents-begin 10475 :contents-end 10479 :post-blank 0 :parent #362) #("PATH" 0 4 (:parent #367))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #362))) (paragraph (:begin 10906 :end 11110 :contents-begin 10906 :contents-end 11109 :post-blank 1 :post-affiliated 10906 :mode nil :granularity nil :parent #354) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #363))) (paragraph (:begin 11110 :end 15385 :contents-begin 11110 :contents-end 15385 :post-blank 0 :post-affiliated 11110 :mode nil :granularity nil :parent #354) #(" which should have the same HASH values " 0 48 (:parent #364)) (italic (:begin 11158 :end 12067 :post-blank 0 :contents-begin 11159 :contents-end 12066 :parent #364) #("gnu/store/7b0qjybvf... etc.\n [07:16]\n profile has a different hash\n but the next ones?\n they're the same\n not sure why profile differs. Do you see the contact with\n mirror.hydra.org? [07:17]\n yeah\n OK, that means you set the key correctly for that one :)\n alright we are at the same state now. You can see most packages need\n to be rebuild because they are no longer cached as binaries on hydra\n [07:18]\n things move fast...\n hehe\n let me also do the same on my laptop - which I have staged before\n [07:19]\n btw, to set the path I often do [07:20]\n export\n PATH=\"/home/wrk" 0 907 (:parent #368))) #(".guix-profile/bin:/home/wrk/.guix-profile/sbin\":$PATH\n to keep things like 'screen' from Debian\n Once past building guix itself that is normally OK [07:21]\n ah, okay\n will do that\n the guix build requires certain versions of tools, so you don't want\n to mix foreign tools in [07:23]\n makes sense [07:24]\n On my laptop I am trying the main updating list of substitutes from\n 'http://hydra.gnu.org'... 10.5% [07:27]\n it is a bit slow, but let's see if there is a difference with the\n mirror\n you can see there are two servers here. Actually with recent daemons,\n if the mirror fails it will try the main server [07:28]\n I documented the use of a caching server here [07:29]\n " 0 800 (:parent #364)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format plain :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil :begin 12867 :end 12932 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n this is exactly what we are doing now\n alrighty [07:35]\n To see if a remote server has a guix server running it should respond\n [07:36]\n lynx " 0 248 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 13180 :end 13213 :contents-begin nil :contents-end nil :post-blank 1 :parent #364)) #("--dump\n Resource not found: /\n\n you see that?\n yes [07:37]\n good. The main hydra server is too slow. So on my laptop I forced\n using the mirror with [07:38]\n env GUIX" 0 224 (:parent #364)) (subscript (:begin 13437 :end 13445 :use-brackets-p nil :contents-begin 13438 :contents-end 13445 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #374))) (subscript (:begin 13445 :end 13450 :use-brackets-p nil :contents-begin 13446 :contents-end 13450 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #375))) #("=../guix-bioinformatics/ ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=\"" 0 116 (:parent #364)) (link (:type "http" :path "//mirror.hydra.gnu.org" :format plain :raw-link "http://mirror.hydra.gnu.org" :application nil :search-option nil :begin 13566 :end 13593 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\"\n\n the list looks the same to me [07:40]\n me too\n note that some packages will be built and some downloaded, right?\n [07:41]\n yes\n atlas is actually a binary on my system [07:43]\n I mean in that list\n so, it should not build. Same as yours?\n yeah, atlas and r-gtable are the ones to be downloaded\n You should not have seen that error ;)\n we should try and install it this way, try [07:44]\n env GUIX" 0 570 (:parent #364)) (subscript (:begin 14163 :end 14171 :use-brackets-p nil :contents-begin 14164 :contents-end 14171 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #379))) (subscript (:begin 14171 :end 14176 :use-brackets-p nil :contents-begin 14172 :contents-end 14176 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #380))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46]\n set CPUs and max-jobs to something sensible\n Does your VM have multiple cores?\n note you can always press Ctrl-C during install\n it doesn't, I'll reboot it and give it another core [07:47]\n Hey [07:48]\n I'm here\n Will be stepping away for some breakfast\n Can you do the same as us\n Can you see the irc log\n Alright\n Yes, I can\n Please email me a copy in five minutes\n user01: so when I use the GN server [07:56]\n env GUIX" 0 659 (:parent #364)) (subscript (:begin 14835 :end 14843 :use-brackets-p nil :contents-begin 14836 :contents-end 14843 :post-blank 0 :parent #364) #("PACKAGE" 0 7 (:parent #382))) (subscript (:begin 14843 :end 14848 :use-brackets-p nil :contents-begin 14844 :contents-end 14848 :post-blank 0 :parent #364) #("PATH" 0 4 (:parent #383))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n --substitute-urls=" 0 114 (:parent #364)) (link (:type "http" :path "//guix.genenetwork.org:8080" :format plain :raw-link "http://guix.genenetwork.org:8080" :application nil :search-option nil :begin 14962 :end 14994 :contents-begin nil :contents-end nil :post-blank 0 :parent #364)) #("\n I don't need to build anything [07:57]\n (this won't work for you, yet)\n to get it to work you need to 'trust' it [07:58]\n but, first get the build going\n I'll have a coffee while you and get building\n yeah it's doing its thing now [08:01]\n cool [08:02]\n in a separate terminal you can try and install with the gn mirror\n" 0 391 (:parent #364)))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #))
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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #183)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1364 :end 1438 :contents-begin 1426 :contents-end 1436 :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 1521 :end 1871 :contents-begin 1521 :contents-end 1870 :post-blank 1 :post-affiliated 1521 :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 1739 :end 1815 :contents-begin 1793 :contents-end 1812 :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 1819 :end 1868 :contents-begin 1858 :contents-end 1866 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 1871 :end 2006 :contents-begin 1871 :contents-end 2006 :post-blank 0 :post-affiliated 1871 :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 1957 :end 2004 :contents-begin 1982 :contents-end 2002 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2007 :end 3390 :pre-blank 1 :contents-begin 2018 :contents-end 3389 :robust-begin 2020 :robust-end 3387 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2007 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2018 :end 2382 :contents-begin 2018 :contents-end 2381 :robust-begin 2018 :robust-end 2379 :post-blank 1 :post-affiliated 2018 :mode section :granularity nil :parent #178) (paragraph (:begin 2018 :end 2381 :contents-begin 2018 :contents-end 2381 :post-blank 0 :post-affiliated 2018 :mode planning :granularity nil :parent #181) #("The quickest way to install GN2 is by using a binary installation\n(tarball or Docker image). These installations are bundled by GNU\nGuix and include all dependencies. You can install GeneNetwork on most\nLinux distributions, including Debian, Ubuntu, Fedora and CentOS,\nprovided you have administrator privileges (root). The alternative is\na Docker installation.\n" 0 363 (:parent #184)))) (headline (:raw-value "Tarball" :begin 2382 :end 3035 :pre-blank 1 :contents-begin 2394 :contents-end 3034 :robust-begin 2396 :robust-end 3032 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2382 :title (#("Tarball" 0 7 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2394 :end 3035 :contents-begin 2394 :contents-end 3034 :robust-begin 2394 :robust-end 3032 :post-blank 1 :post-affiliated 2394 :mode section :granularity nil :parent #182) (paragraph (:begin 2394 :end 2541 :contents-begin 2394 :contents-end 2540 :post-blank 1 :post-affiliated 2394 :mode planning :granularity nil :parent #185) #("Download the ~800Mb tarball from\n" 0 33 (:parent #188)) (link (:type "http" :path "//files.genenetwork.org/software/binary_tarball/" :format bracket :raw-link "http://files.genenetwork.org/software/binary_tarball/" :application nil :search-option nil :begin 2427 :end 2484 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(". Validate the checksum and\nunpack to root, for example\n" 0 56 (:parent #188))) (fixed-width (:begin 2541 :end 2643 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2541 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2643 :end 2691 :contents-begin 2643 :contents-end 2690 :post-blank 1 :post-affiliated 2643 :mode nil :granularity nil :parent #185) #("Now you shoud be able to start the server with\n" 0 47 (:parent #190))) (fixed-width (:begin 2691 :end 2729 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2691 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2729 :end 2856 :contents-begin 2729 :contents-end 2855 :post-blank 1 :post-affiliated 2729 :mode nil :granularity nil :parent #185) #("When the server stops with a MySQL error " 0 41 (:parent #192)) (link (:type "custom-id" :path "run-mysql-server" :format bracket :raw-link "#run-mysql-server" :application nil :search-option nil :begin 2770 :end 2809 :contents-begin 2791 :contents-end 2807 :post-blank 0 :parent #192) #("Run MySQL server" 0 16 (:parent #196))) #("\nand set SQL" 0 12 (:parent #192)) (subscript (:begin 2821 :end 2826 :use-brackets-p nil :contents-begin 2822 :contents-end 2825 :post-blank 1 :parent #192) #("URI" 0 3 (:parent #198))) #("to point at it. For example:\n" 0 29 (:parent #192))) (fixed-width (:begin 2856 :end 2923 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 2856 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2923 :end 3034 :contents-begin 2923 :contents-end 3034 :post-blank 0 :post-affiliated 2923 :mode nil :granularity nil :parent #185) #("See also " 0 9 (:parent #194)) (link (:type "custom-id" :path "mysql-cant-connect-server-through-socket-error" :format bracket :raw-link "#mysql-cant-connect-server-through-socket-error" :application nil :search-option nil :begin 2932 :end 3032 :contents-begin 2983 :contents-end 3030 :post-blank 0 :parent #194) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #198))) #(".\n" 0 2 (:parent #194))))) (headline (:raw-value "Docker" :begin 3035 :end 3244 :pre-blank 1 :contents-begin 3046 :contents-end 3243 :robust-begin 3048 :robust-end 3241 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3035 :title (#("Docker" 0 6 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 3046 :end 3244 :contents-begin 3046 :contents-end 3243 :robust-begin 3046 :robust-end 3241 :post-blank 1 :post-affiliated 3046 :mode section :granularity nil :parent #183) (paragraph (:begin 3046 :end 3243 :contents-begin 3046 :contents-end 3243 :post-blank 0 :post-affiliated 3046 :mode planning :granularity nil :parent #186) #("Docker images are also available through\n" 0 41 (:parent #189)) (link (:type "http" :path "//files.genenetwork.org/software/" :format bracket :raw-link "http://files.genenetwork.org/software/" :application nil :search-option nil :begin 3087 :end 3129 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(". Validate the checksum and run\nwith " 0 37 (:parent #189)) (link (:type "https" :path "//docs.docker.com/engine/reference/commandline/load/" :format bracket :raw-link "https://docs.docker.com/engine/reference/commandline/load/" :application nil :search-option nil :begin 3166 :end 3241 :contents-begin 3228 :contents-end 3239 :post-blank 0 :parent #189) #("Docker load" 0 11 (:parent #195))) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "With source" :begin 3244 :end 3390 :pre-blank 1 :contents-begin 3260 :contents-end 3389 :robust-begin 3262 :robust-end 3387 :level 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 (#("With source" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 3260 :end 3390 :contents-begin 3260 :contents-end 3389 :robust-begin 3260 :robust-end 3387 :post-blank 1 :post-affiliated 3260 :mode section :granularity nil :parent #184) (paragraph (:begin 3260 :end 3389 :contents-begin 3260 :contents-end 3389 :post-blank 0 :post-affiliated 3260 :mode planning :granularity nil :parent #187) #("For more elaborate installation instructions on deploying GeneNetwork from\nsource see " 0 86 (:parent #190)) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 3346 :end 3387 :contents-begin 3368 :contents-end 3385 :post-blank 0 :parent #190) #("Source deployment" 0 17 (:parent #194))) #(".\n" 0 2 (:parent #190)))))) (headline (:raw-value "Running GN2" :begin 3390 :end 3871 :pre-blank 1 :contents-begin 3405 :contents-end 3870 :robust-begin 3407 :robust-end 3868 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3390 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 3405 :end 3871 :contents-begin 3405 :contents-end 3870 :robust-begin 3405 :robust-end 3868 :post-blank 1 :post-affiliated 3405 :mode section :granularity nil :parent #179) (paragraph (:begin 3405 :end 3600 :contents-begin 3405 :contents-end 3599 :post-blank 1 :post-affiliated 3405 :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 3458 :end 3509 :contents-begin 3488 :contents-end 3507 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 3495 :end 3507 :use-brackets-p nil :contents-begin 3496 :contents-end 3507 :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 3600 :end 3630 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3600 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3630 :end 3708 :contents-begin 3630 :contents-end 3707 :post-blank 1 :post-affiliated 3630 :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 3708 :end 3791 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3708 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3791 :end 3870 :contents-begin 3791 :contents-end 3870 :post-blank 0 :post-affiliated 3791 :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 MySQL server" :begin 3871 :end 5896 :pre-blank 0 :contents-begin 3890 :contents-end 5895 :robust-begin 3892 :robust-end 5893 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3871 :title (#("Run MySQL server" 0 16 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 3890 :end 4364 :pre-blank 1 :contents-begin 3922 :contents-end 4363 :robust-begin 3924 :robust-end 4361 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3890 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 3922 :end 4364 :contents-begin 3922 :contents-end 4363 :robust-begin 3922 :robust-end 4361 :post-blank 1 :post-affiliated 3922 :mode section :granularity nil :parent #183) (paragraph (:begin 3922 :end 4057 :contents-begin 3922 :contents-end 4056 :post-blank 1 :post-affiliated 3922 :mode planning :granularity nil :parent #186) #("These are the steps you can take to install a fresh installation of\nmysql (which comes as part of the GNU Guix genenetwork2 install).\n" 0 134 (:parent #189))) (paragraph (:begin 4057 :end 4084 :contents-begin 4057 :contents-end 4083 :post-blank 1 :post-affiliated 4057 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #190))) (fixed-width (:begin 4084 :end 4332 :value " adduser mysql && addgroup mysql\n mysqld --datadir=/var/mysql --initialize-insecure\n mkdir -p /var/run/mysqld\n chown mysql.mysql ~/mysql /var/run/mysqld\n su mysql -c mysqld --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" :post-blank 2 :post-affiliated 4084 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4332 :end 4363 :contents-begin 4332 :contents-end 4363 :post-blank 0 :post-affiliated 4332 :mode nil :granularity nil :parent #186) #("/etc/my.cnf\n[mysqld]\nuser=root\n" 0 31 (:parent #192))))) (headline (:raw-value "Load the small database in MySQL" :begin 4364 :end 5896 :pre-blank 1 :contents-begin 4401 :contents-end 5895 :robust-begin 4403 :robust-end 5893 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4364 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 4401 :end 5896 :contents-begin 4401 :contents-end 5895 :robust-begin 4401 :robust-end 5893 :post-blank 1 :post-affiliated 4401 :mode section :granularity nil :parent #184) (paragraph (:begin 4401 :end 4708 :contents-begin 4401 :contents-end 4707 :post-blank 1 :post-affiliated 4401 :mode planning :granularity nil :parent #187) #("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 #190)) (subscript (:begin 4564 :end 4571 :use-brackets-p nil :contents-begin 4565 :contents-end 4571 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 4571 :end 4573 :use-brackets-p nil :contents-begin 4572 :contents-end 4573 :post-blank 0 :parent #190) #("s" 0 1 (:parent #195))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #190)) (subscript (:begin 4649 :end 4656 :use-brackets-p nil :contents-begin 4650 :contents-end 4656 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 4656 :end 4662 :use-brackets-p nil :contents-begin 4657 :contents-end 4662 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 4708 :end 4736 :contents-begin 4708 :contents-end 4735 :post-blank 1 :post-affiliated 4708 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 4736 :end 4784 :contents-begin 4736 :contents-end 4783 :post-blank 1 :post-affiliated 4736 :mode nil :granularity nil :parent #187) (link (:type "http" :path "//files.genenetwork.org/raw_database/" :format bracket :raw-link "http://files.genenetwork.org/raw_database/" :application nil :search-option nil :begin 4736 :end 4782 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 4784 :end 4843 :contents-begin 4784 :contents-end 4842 :post-blank 1 :post-affiliated 4784 :mode nil :granularity nil :parent #187) (link (:type "https" :path "//s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :format bracket :raw-link "https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip" :application nil :search-option nil :begin 4784 :end 4841 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 4843 :end 4862 :contents-begin 4843 :contents-end 4861 :post-blank 1 :post-affiliated 4843 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 4862 :end 4933 :contents-begin 4862 :contents-end 4932 :post-blank 1 :post-affiliated 4862 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 4933 :end 5034 :value "cd ~/mysql\nchown -R mysql:mysql db_webqtl_s/\nchmod 700 db_webqtl_s/\nchmod 660 db_webqtl_s/*" :post-blank 2 :post-affiliated 4933 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5034 :end 5081 :contents-begin 5034 :contents-end 5080 :post-blank 1 :post-affiliated 5034 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5081 :end 5098 :value "myslq -u root" :post-blank 2 :post-affiliated 5081 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5098 :end 5103 :contents-begin 5098 :contents-end 5102 :post-blank 1 :post-affiliated 5098 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 5103 :end 5329 :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 5103 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5329 :end 5394 :contents-begin 5329 :contents-end 5393 :post-blank 1 :post-affiliated 5329 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 5394 :end 5493 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 5394 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5493 :end 5600 :contents-begin 5493 :contents-end 5599 :post-blank 1 :post-affiliated 5493 :mode nil :granularity nil :parent #187) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #203))) (paragraph (:begin 5600 :end 5763 :contents-begin 5600 :contents-end 5762 :post-blank 1 :post-affiliated 5600 :mode nil :granularity nil :parent #187) #("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 #204))) (paragraph (:begin 5763 :end 5895 :contents-begin 5763 :contents-end 5895 :post-blank 0 :post-affiliated 5763 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 5814 :end 5821 :use-brackets-p nil :contents-begin 5815 :contents-end 5821 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 5821 :end 5823 :use-brackets-p nil :contents-begin 5822 :contents-end 5823 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 5862 :end 5875 :use-brackets-p nil :contents-begin 5863 :contents-end 5874 :post-blank 1 :parent #205) #("settings.py" 0 11 (:parent #212))) #("to match your path.\n" 0 20 (:parent #205)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 5896 :end 6060 :pre-blank 1 :contents-begin 5920 :contents-end 6059 :robust-begin 5922 :robust-end 6057 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5896 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 5920 :end 6060 :contents-begin 5920 :contents-end 6059 :robust-begin 5920 :robust-end 6057 :post-blank 1 :post-affiliated 5920 :mode section :granularity nil :parent #181) (paragraph (:begin 5920 :end 5981 :contents-begin 5920 :contents-end 5980 :post-blank 1 :post-affiliated 5920 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 5981 :end 6059 :contents-begin 6011 :contents-end 6059 :post-blank 0 :post-affiliated 6011 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #184) (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 6011 :end 6058 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #("\n" 0 1 (:parent #188))))) (headline (:raw-value "Working with the GN2 source code" :begin 6060 :end 6122 :pre-blank 1 :contents-begin 6096 :contents-end 6121 :robust-begin 6098 :robust-end 6119 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6060 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 6096 :end 6122 :contents-begin 6096 :contents-end 6121 :robust-begin 6096 :robust-end 6119 :post-blank 1 :post-affiliated 6096 :mode section :granularity nil :parent #182) (paragraph (:begin 6096 :end 6121 :contents-begin 6096 :contents-end 6121 :post-blank 0 :post-affiliated 6096 :mode planning :granularity nil :parent #185) #("See " 0 4 (:parent #188)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6100 :end 6119 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Trouble shooting" :begin 6122 :end 8347 :pre-blank 1 :contents-begin 6142 :contents-end 8346 :robust-begin 6144 :robust-end 8344 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6122 :title (#("Trouble shooting" 0 16 (:parent #183))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 6142 :end 6676 :pre-blank 1 :contents-begin 6182 :contents-end 6676 :robust-begin 6184 :robust-end 6674 :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 6142 :title (#("ImportError: No module named jinja2" 0 35 (:parent #186))) :mode section :granularity nil :parent #183) (section (:begin 6182 :end 6676 :contents-begin 6182 :contents-end 6676 :robust-begin 6182 :robust-end 6674 :post-blank 0 :post-affiliated 6182 :mode section :granularity nil :parent #186) (paragraph (:begin 6182 :end 6417 :contents-begin 6182 :contents-end 6416 :post-blank 1 :post-affiliated 6182 :mode planning :granularity nil :parent #189) #("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 #192)) (subscript (:begin 6349 :end 6355 :use-brackets-p nil :contents-begin 6350 :contents-end 6354 :post-blank 1 :parent #192) #("PATH" 0 4 (:parent #196))) #("and R" 0 5 (:parent #192)) (subscript (:begin 6360 :end 6365 :use-brackets-p nil :contents-begin 6361 :contents-end 6365 :post-blank 0 :parent #192) #("LIBS" 0 4 (:parent #198))) (subscript (:begin 6365 :end 6371 :use-brackets-p nil :contents-begin 6366 :contents-end 6370 :post-blank 1 :parent #192) #("SITE" 0 4 (:parent #199))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #192))) (fixed-width (:begin 6417 :end 6448 :value "guix package --search-paths" :post-blank 2 :post-affiliated 6417 :mode nil :granularity nil :parent #189)) (paragraph (:begin 6448 :end 6464 :contents-begin 6448 :contents-end 6463 :post-blank 1 :post-affiliated 6448 :mode nil :granularity nil :parent #189) #("On one system:\n" 0 15 (:parent #194))) (fixed-width (:begin 6464 :end 6652 :value "export PYTHONPATH=\"$HOME/.guix-profile/lib/python2.7/site-packages\"\nexport R_LIBS_SITE=\"$HOME/.guix-profile/site-library/\"\nexport GEM_PATH=\"$HOME/.guix-profile/lib/ruby/gems/2.2.0\"" :post-blank 2 :post-affiliated 6464 :mode nil :granularity nil :parent #189)) (paragraph (:begin 6652 :end 6676 :contents-begin 6652 :contents-end 6676 :post-blank 0 :post-affiliated 6652 :mode nil :granularity nil :parent #189) #("and perhaps a few more.\n" 0 24 (:parent #196))))) (headline (:raw-value "ERROR: can not find directory $HOME/gn2_data" :begin 6676 :end 6947 :pre-blank 1 :contents-begin 6725 :contents-end 6946 :robust-begin 6727 :robust-end 6944 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6676 :title (#("ERROR: can not find directory $HOME/gn2" 0 39 (:parent #187)) (subscript (:begin 6718 :end 6723 :use-brackets-p nil :contents-begin 6719 :contents-end 6723 :post-blank 0 :parent #187) #("data" 0 4 (:parent #229)))) :mode nil :granularity nil :parent #183) (section (:begin 6725 :end 6947 :contents-begin 6725 :contents-end 6946 :robust-begin 6725 :robust-end 6944 :post-blank 1 :post-affiliated 6725 :mode section :granularity nil :parent #187) (paragraph (:begin 6725 :end 6946 :contents-begin 6725 :contents-end 6946 :post-blank 0 :post-affiliated 6725 :mode planning :granularity nil :parent #190) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #193)) (subscript (:begin 6774 :end 6779 :use-brackets-p nil :contents-begin 6775 :contents-end 6779 :post-blank 0 :parent #193) #("data" 0 4 (:parent #197))) #(". 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 #193)) (subscript (:begin 6903 :end 6916 :use-brackets-p nil :contents-begin 6904 :contents-end 6915 :post-blank 1 :parent #193) #("settings.py" 0 11 (:parent #199))) #("(see above in\nthis document).\n" 0 30 (:parent #193))))) (headline (:raw-value "Can't run a module" :begin 6947 :end 7181 :pre-blank 1 :contents-begin 6970 :contents-end 7181 :robust-begin 6972 :robust-end 7179 :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 6947 :title (#("Can't run a module" 0 18 (:parent #188))) :mode nil :granularity nil :parent #183) (section (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :robust-begin 6970 :robust-end 7179 :post-blank 0 :post-affiliated 6970 :mode section :granularity nil :parent #188) (paragraph (:begin 6970 :end 7181 :contents-begin 6970 :contents-end 7181 :post-blank 0 :post-affiliated 6970 :mode planning :granularity nil :parent #191) #("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 #194))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 7181 :end 7682 :pre-blank 1 :contents-begin 7213 :contents-end 7681 :robust-begin 7215 :robust-end 7679 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7181 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #189))) :mode nil :granularity nil :parent #183) (section (:begin 7213 :end 7682 :contents-begin 7213 :contents-end 7681 :robust-begin 7213 :robust-end 7679 :post-blank 1 :post-affiliated 7213 :mode section :granularity nil :parent #189) (paragraph (:begin 7213 :end 7225 :contents-begin 7213 :contents-end 7224 :post-blank 1 :post-affiliated 7213 :mode planning :granularity nil :parent #192) #("This error\n" 0 11 (:parent #195))) (fixed-width (:begin 7225 :end 7305 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 7225 :mode nil :granularity nil :parent #192)) (paragraph (:begin 7305 :end 7436 :contents-begin 7305 :contents-end 7435 :post-blank 1 :post-affiliated 7305 :mode nil :granularity nil :parent #192) #("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 #197))) (paragraph (:begin 7436 :end 7681 :contents-begin 7436 :contents-end 7681 :post-blank 0 :post-affiliated 7436 :mode nil :granularity nil :parent #192) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #198)) (subscript (:begin 7499 :end 7504 :use-brackets-p nil :contents-begin 7500 :contents-end 7504 :post-blank 0 :parent #198) #("LIBS" 0 4 (:parent #202))) (subscript (:begin 7504 :end 7509 :use-brackets-p nil :contents-begin 7505 :contents-end 7509 :post-blank 0 :parent #198) #("SITE" 0 4 (:parent #203))) #(". 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 #198))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 7682 :end 8347 :pre-blank 1 :contents-begin 7734 :contents-end 8346 :robust-begin 7736 :robust-end 8344 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7682 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #190))) :mode nil :granularity nil :parent #183) (section (:begin 7734 :end 8347 :contents-begin 7734 :contents-end 8346 :robust-begin 7734 :robust-end 8344 :post-blank 1 :post-affiliated 7734 :mode section :granularity nil :parent #190) (paragraph (:begin 7734 :end 7755 :contents-begin 7734 :contents-end 7754 :post-blank 1 :post-affiliated 7734 :mode planning :granularity nil :parent #193) #("The following error\n" 0 20 (:parent #196))) (fixed-width (:begin 7755 :end 7950 :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 7755 :mode nil :granularity nil :parent #193)) (paragraph (:begin 7950 :end 8108 :contents-begin 7950 :contents-end 8107 :post-blank 1 :post-affiliated 7950 :mode nil :granularity nil :parent #193) #("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 #198))) (fixed-width (:begin 8108 :end 8130 :value "mysql -h localhost" :post-blank 2 :post-affiliated 8108 :mode nil :granularity nil :parent #193)) (paragraph (:begin 8130 :end 8187 :contents-begin 8130 :contents-end 8186 :post-blank 1 :post-affiliated 8130 :mode nil :granularity nil :parent #193) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #200))) (fixed-width (:begin 8187 :end 8209 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 8187 :mode nil :granularity nil :parent #193)) (paragraph (:begin 8209 :end 8280 :contents-begin 8209 :contents-end 8279 :post-blank 1 :post-affiliated 8209 :mode nil :granularity nil :parent #193) #("if that works run genenetwork after setting SQL" 0 47 (:parent #202)) (subscript (:begin 8256 :end 8261 :use-brackets-p nil :contents-begin 8257 :contents-end 8260 :post-blank 1 :parent #202) #("URI" 0 3 (:parent #206))) #("to something like\n" 0 18 (:parent #202))) (fixed-width (:begin 8280 :end 8346 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 8280 :mode nil :granularity nil :parent #193))))) (headline (:raw-value "Read more" :begin 8347 :end 8497 :pre-blank 1 :contents-begin 8360 :contents-end 8496 :robust-begin 8362 :robust-end 8494 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8347 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 8360 :end 8497 :contents-begin 8360 :contents-end 8496 :robust-begin 8360 :robust-end 8494 :post-blank 1 :post-affiliated 8360 :mode section :granularity nil :parent #184) (paragraph (:begin 8360 :end 8496 :contents-begin 8360 :contents-end 8496 :post-blank 0 :post-affiliated 8360 :mode planning :granularity nil :parent #187) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #190)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 8415 :end 8435 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #190))))) (headline (:raw-value "IRC session" :begin 8497 :end 15385 :pre-blank 1 :contents-begin 8512 :contents-end 15385 :robust-begin 8514 :robust-end 15383 :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 8497 :title (#("IRC session" 0 11 (:parent #185))) :mode nil :granularity nil :parent #172) (section (:begin 8512 :end 15385 :contents-begin 8512 :contents-end 15385 :robust-begin 8512 :robust-end 15383 :post-blank 0 :post-affiliated 8512 :mode section :granularity nil :parent #185) (paragraph (:begin 8512 :end 8621 :contents-begin 8512 :contents-end 8620 :post-blank 1 :post-affiliated 8512 :mode planning :granularity nil :parent #188) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #191))) (paragraph (:begin 8621 :end 9182 :contents-begin 8621 :contents-end 9181 :post-blank 1 :post-affiliated 8621 :mode nil :granularity nil :parent #188) #("#+begin" 0 7 (:parent #192)) (subscript (:begin 8628 :end 8632 :use-brackets-p nil :contents-begin 8629 :contents-end 8632 :post-blank 0 :parent #192) #("src" 0 3 (:parent #196))) #("\n time to get binary install sorted :) [07:03]\n Guix is designed for distributed installation servers\n we have one on guix.genenetwork.org\n it contains all the prebuild packages\n for GN\n okay [07:04]\n let's step back however [07:05]\n I presume the environment is set with all guix package --search-paths\n right?\n yep\n set to the ones in ~/.guix-profile/\n good, and you are in gn-deploy-guix repo [07:06]\n yep [07:07]\n git log shows\n" 0 549 (:parent #192))) (paragraph (:begin 9182 :end 9272 :contents-begin 9182 :contents-end 9271 :post-blank 1 :post-affiliated 9182 :mode nil :granularity nil :parent #188) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #193))) (paragraph (:begin 9272 :end 9417 :contents-begin 9272 :contents-end 9416 :post-blank 1 :post-affiliated 9272 :mode nil :granularity nil :parent #188) #(" yes\n env GUIX" 0 30 (:parent #194)) (subscript (:begin 9302 :end 9310 :use-brackets-p nil :contents-begin 9303 :contents-end 9310 :post-blank 0 :parent #194) #("PACKAGE" 0 7 (:parent #198))) (subscript (:begin 9310 :end 9315 :use-brackets-p nil :contents-begin 9311 :contents-end 9315 :post-blank 0 :parent #194) #("PATH" 0 4 (:parent #199))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #194))) (paragraph (:begin 9417 :end 9713 :contents-begin 9417 :contents-end 9712 :post-blank 1 :post-affiliated 9417 :mode nil :granularity nil :parent #188) #("genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2\ngenenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4\ngenenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4\n" 0 295 (:parent #195))) (paragraph (:begin 9713 :end 10906 :contents-begin 9713 :contents-end 10905 :post-blank 1 :post-affiliated 9713 :mode nil :granularity nil :parent #188) #(" yeah [07:09]\n OK, we are in sync. This means we should be able to install the exact\n same software\n I need to start up my guix daemon - I usually run it in a screen\n screen -S guix-daemon\n hah, I don't have screen installed yet [07:11]\n comes with guix ;) [07:12]\n no worries, you can run it any way you want\n $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild\n then something's weird, because it says I don't have it\n oh, you need to install it first [07:13]\n guix package -A screen\n screen 4.3.1 out gnu/packages/screen.scm:34:2\n but you can skip this install, for now\n alright [07:14]\n env GUIX" 0 753 (:parent #196)) (subscript (:begin 10466 :end 10474 :use-brackets-p nil :contents-begin 10467 :contents-end 10474 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 10474 :end 10479 :use-brackets-p nil :contents-begin 10475 :contents-end 10479 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -i genenetwork2 --dry-run\n substitute: updating list of substitutes from\n 'https://mirror.hydra.gnu.org'... 79.1%\n you see that?\n followed by [07:15]\nsubstitute: updating list of substitutes from\n'https://hydra.gnu.org'... 100.0%\nThe following derivations would be built:\n /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv\n" 0 426 (:parent #196))) (paragraph (:begin 10906 :end 11110 :contents-begin 10906 :contents-end 11109 :post-blank 1 :post-affiliated 10906 :mode nil :granularity nil :parent #188) #("/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv\n /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv\n /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv\n" 0 203 (:parent #197))) (paragraph (:begin 11110 :end 15385 :contents-begin 11110 :contents-end 15385 :post-blank 0 :post-affiliated 11110 :mode nil :granularity nil :parent #188) #("
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