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 1557 :end 1631 :contents-begin 1619 :contents-end 1629 :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 1714 :end 2064 :contents-begin 1714 :contents-end 2063 :post-blank 1 :post-affiliated 1714 :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 1932 :end 2008 :contents-begin 1986 :contents-end 2005 :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 2012 :end 2061 :contents-begin 2051 :contents-end 2059 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2064 :end 2199 :contents-begin 2064 :contents-end 2199 :post-blank 0 :post-affiliated 2064 :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 2150 :end 2197 :contents-begin 2175 :contents-end 2195 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2200 :end 3583 :pre-blank 1 :contents-begin 2211 :contents-end 3582 :robust-begin 2213 :robust-end 3580 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2200 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2211 :end 2575 :contents-begin 2211 :contents-end 2574 :robust-begin 2211 :robust-end 2572 :post-blank 1 :post-affiliated 2211 :mode section :granularity nil :parent #178) (paragraph (:begin 2211 :end 2574 :contents-begin 2211 :contents-end 2574 :post-blank 0 :post-affiliated 2211 :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 2575 :end 3228 :pre-blank 1 :contents-begin 2587 :contents-end 3227 :robust-begin 2589 :robust-end 3225 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2575 :title (#("Tarball" 0 7 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2587 :end 3228 :contents-begin 2587 :contents-end 3227 :robust-begin 2587 :robust-end 3225 :post-blank 1 :post-affiliated 2587 :mode section :granularity nil :parent #182) (paragraph (:begin 2587 :end 2734 :contents-begin 2587 :contents-end 2733 :post-blank 1 :post-affiliated 2587 :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 2620 :end 2677 :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 2734 :end 2836 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2734 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2836 :end 2884 :contents-begin 2836 :contents-end 2883 :post-blank 1 :post-affiliated 2836 :mode nil :granularity nil :parent #185) #("Now you shoud be able to start the server with\n" 0 47 (:parent #190))) (fixed-width (:begin 2884 :end 2922 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2884 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2922 :end 3049 :contents-begin 2922 :contents-end 3048 :post-blank 1 :post-affiliated 2922 :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 2963 :end 3002 :contents-begin 2984 :contents-end 3000 :post-blank 0 :parent #192) #("Run MySQL server" 0 16 (:parent #196))) #("\nand set SQL" 0 12 (:parent #192)) (subscript (:begin 3014 :end 3019 :use-brackets-p nil :contents-begin 3015 :contents-end 3018 :post-blank 1 :parent #192) #("URI" 0 3 (:parent #198))) #("to point at it. For example:\n" 0 29 (:parent #192))) (fixed-width (:begin 3049 :end 3116 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 3049 :mode nil :granularity nil :parent #185)) (paragraph (:begin 3116 :end 3227 :contents-begin 3116 :contents-end 3227 :post-blank 0 :post-affiliated 3116 :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 3125 :end 3225 :contents-begin 3176 :contents-end 3223 :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 3228 :end 3437 :pre-blank 1 :contents-begin 3239 :contents-end 3436 :robust-begin 3241 :robust-end 3434 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3228 :title (#("Docker" 0 6 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 3239 :end 3437 :contents-begin 3239 :contents-end 3436 :robust-begin 3239 :robust-end 3434 :post-blank 1 :post-affiliated 3239 :mode section :granularity nil :parent #183) (paragraph (:begin 3239 :end 3436 :contents-begin 3239 :contents-end 3436 :post-blank 0 :post-affiliated 3239 :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 3280 :end 3322 :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 3359 :end 3434 :contents-begin 3421 :contents-end 3432 :post-blank 0 :parent #189) #("Docker load" 0 11 (:parent #195))) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "With source" :begin 3437 :end 3583 :pre-blank 1 :contents-begin 3453 :contents-end 3582 :robust-begin 3455 :robust-end 3580 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3437 :title (#("With source" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 3453 :end 3583 :contents-begin 3453 :contents-end 3582 :robust-begin 3453 :robust-end 3580 :post-blank 1 :post-affiliated 3453 :mode section :granularity nil :parent #184) (paragraph (:begin 3453 :end 3582 :contents-begin 3453 :contents-end 3582 :post-blank 0 :post-affiliated 3453 :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 3539 :end 3580 :contents-begin 3561 :contents-end 3578 :post-blank 0 :parent #190) #("Source deployment" 0 17 (:parent #194))) #(".\n" 0 2 (:parent #190)))))) (headline (:raw-value "Running GN2" :begin 3583 :end 4064 :pre-blank 1 :contents-begin 3598 :contents-end 4063 :robust-begin 3600 :robust-end 4061 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3583 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 3598 :end 4064 :contents-begin 3598 :contents-end 4063 :robust-begin 3598 :robust-end 4061 :post-blank 1 :post-affiliated 3598 :mode section :granularity nil :parent #179) (paragraph (:begin 3598 :end 3793 :contents-begin 3598 :contents-end 3792 :post-blank 1 :post-affiliated 3598 :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 3651 :end 3702 :contents-begin 3681 :contents-end 3700 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 3688 :end 3700 :use-brackets-p nil :contents-begin 3689 :contents-end 3700 :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 3793 :end 3823 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3793 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3823 :end 3901 :contents-begin 3823 :contents-end 3900 :post-blank 1 :post-affiliated 3823 :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 3901 :end 3984 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3901 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3984 :end 4063 :contents-begin 3984 :contents-end 4063 :post-blank 0 :post-affiliated 3984 :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 4064 :end 6699 :pre-blank 0 :contents-begin 4083 :contents-end 6698 :robust-begin 4085 :robust-end 6696 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4064 :title (#("Run MySQL server" 0 16 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 4083 :end 5167 :pre-blank 1 :contents-begin 4115 :contents-end 5166 :robust-begin 4117 :robust-end 5164 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4083 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 4115 :end 5167 :contents-begin 4115 :contents-end 5166 :robust-begin 4115 :robust-end 5164 :post-blank 1 :post-affiliated 4115 :mode section :granularity nil :parent #183) (paragraph (:begin 4115 :end 4250 :contents-begin 4115 :contents-end 4249 :post-blank 1 :post-affiliated 4115 :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 4250 :end 4277 :contents-begin 4250 :contents-end 4276 :post-blank 1 :post-affiliated 4250 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #190))) (src-block (:language "bash" :switches nil :parameters nil :begin 4277 :end 4535 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mysql && addgroup mysql\nmysqld --datadir=/var/mysql --initialize-insecure\nmkdir -p /var/run/mysqld\nchown mysql.mysql ~/mysql /var/run/mysqld\nmysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 4277 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4535 :end 4583 :contents-begin 4535 :contents-end 4582 :post-blank 1 :post-affiliated 4535 :mode nil :granularity nil :parent #186) #("If you want to run as root you may have to set\n" 0 47 (:parent #192))) (fixed-width (:begin 4583 :end 4621 :value "/etc/my.cnf\n[mysqld]\nuser=root" :post-blank 2 :post-affiliated 4583 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4621 :end 4690 :contents-begin 4621 :contents-end 4689 :post-blank 1 :post-affiliated 4621 :mode nil :granularity nil :parent #186) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #194))) (fixed-width (:begin 4690 :end 4799 :value "mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log" :post-blank 2 :post-affiliated 4690 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4799 :end 4875 :contents-begin 4799 :contents-end 4874 :post-blank 1 :post-affiliated 4799 :mode nil :granularity nil :parent #186) #("Other tips are that Guix installs mysqld in your profile, so this may work\n" 0 75 (:parent #196))) (fixed-width (:begin 4875 :end 4979 :value "/home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql" :post-blank 2 :post-affiliated 4875 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4979 :end 5006 :contents-begin 4979 :contents-end 5005 :post-blank 1 :post-affiliated 4979 :mode nil :granularity nil :parent #186) #("When you get errors like:\n" 0 26 (:parent #198))) (fixed-width (:begin 5006 :end 5118 :value "qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 5006 :mode nil :granularity nil :parent #186)) (paragraph (:begin 5118 :end 5139 :contents-begin 5118 :contents-end 5138 :post-blank 1 :post-affiliated 5118 :mode nil :granularity nil :parent #186) #("you may need to set\n" 0 20 (:parent #200))) (fixed-width (:begin 5139 :end 5166 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 5139 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "Load the small database in MySQL" :begin 5167 :end 6699 :pre-blank 1 :contents-begin 5204 :contents-end 6698 :robust-begin 5206 :robust-end 6696 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5167 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 5204 :end 6699 :contents-begin 5204 :contents-end 6698 :robust-begin 5204 :robust-end 6696 :post-blank 1 :post-affiliated 5204 :mode section :granularity nil :parent #184) (paragraph (:begin 5204 :end 5511 :contents-begin 5204 :contents-end 5510 :post-blank 1 :post-affiliated 5204 :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 5367 :end 5374 :use-brackets-p nil :contents-begin 5368 :contents-end 5374 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 5374 :end 5376 :use-brackets-p nil :contents-begin 5375 :contents-end 5376 :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 5452 :end 5459 :use-brackets-p nil :contents-begin 5453 :contents-end 5459 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 5459 :end 5465 :use-brackets-p nil :contents-begin 5460 :contents-end 5465 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 5511 :end 5539 :contents-begin 5511 :contents-end 5538 :post-blank 1 :post-affiliated 5511 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 5539 :end 5587 :contents-begin 5539 :contents-end 5586 :post-blank 1 :post-affiliated 5539 :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 5539 :end 5585 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 5587 :end 5646 :contents-begin 5587 :contents-end 5645 :post-blank 1 :post-affiliated 5587 :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 5587 :end 5644 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 5646 :end 5665 :contents-begin 5646 :contents-end 5664 :post-blank 1 :post-affiliated 5646 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 5665 :end 5736 :contents-begin 5665 :contents-end 5735 :post-blank 1 :post-affiliated 5665 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 5736 :end 5837 :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 5736 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5837 :end 5884 :contents-begin 5837 :contents-end 5883 :post-blank 1 :post-affiliated 5837 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5884 :end 5901 :value "myslq -u root" :post-blank 2 :post-affiliated 5884 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5901 :end 5906 :contents-begin 5901 :contents-end 5905 :post-blank 1 :post-affiliated 5901 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 5906 :end 6132 :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 5906 :mode nil :granularity nil :parent #187)) (paragraph (:begin 6132 :end 6197 :contents-begin 6132 :contents-end 6196 :post-blank 1 :post-affiliated 6132 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 6197 :end 6296 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 6197 :mode nil :granularity nil :parent #187)) (paragraph (:begin 6296 :end 6403 :contents-begin 6296 :contents-end 6402 :post-blank 1 :post-affiliated 6296 :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 6403 :end 6566 :contents-begin 6403 :contents-end 6565 :post-blank 1 :post-affiliated 6403 :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 6566 :end 6698 :contents-begin 6566 :contents-end 6698 :post-blank 0 :post-affiliated 6566 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 6617 :end 6624 :use-brackets-p nil :contents-begin 6618 :contents-end 6624 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 6624 :end 6626 :use-brackets-p nil :contents-begin 6625 :contents-end 6626 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 6665 :end 6678 :use-brackets-p nil :contents-begin 6666 :contents-end 6677 :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 6699 :end 6863 :pre-blank 1 :contents-begin 6723 :contents-end 6862 :robust-begin 6725 :robust-end 6860 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6699 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 6723 :end 6863 :contents-begin 6723 :contents-end 6862 :robust-begin 6723 :robust-end 6860 :post-blank 1 :post-affiliated 6723 :mode section :granularity nil :parent #181) (paragraph (:begin 6723 :end 6784 :contents-begin 6723 :contents-end 6783 :post-blank 1 :post-affiliated 6723 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 6784 :end 6862 :contents-begin 6814 :contents-end 6862 :post-blank 0 :post-affiliated 6814 :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 6814 :end 6861 :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 6863 :end 6925 :pre-blank 1 :contents-begin 6899 :contents-end 6924 :robust-begin 6901 :robust-end 6922 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6863 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 6899 :end 6925 :contents-begin 6899 :contents-end 6924 :robust-begin 6899 :robust-end 6922 :post-blank 1 :post-affiliated 6899 :mode section :granularity nil :parent #182) (paragraph (:begin 6899 :end 6924 :contents-begin 6899 :contents-end 6924 :post-blank 0 :post-affiliated 6899 :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 6903 :end 6922 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Running ElasticSearch" :begin 6925 :end 7675 :pre-blank 1 :contents-begin 6950 :contents-end 7674 :robust-begin 6952 :robust-end 7672 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6925 :title (#("Running ElasticSearch" 0 21 (:parent #183))) :parent #172 :cached t :granularity nil) (section (:begin 6950 :end 7134 :contents-begin 6950 :contents-end 7132 :robust-begin 6950 :robust-end 7130 :post-blank 2 :post-affiliated 6950 :mode section :granularity nil :parent #183) (paragraph (:begin 6950 :end 7132 :contents-begin 6950 :contents-end 7132 :post-blank 0 :post-affiliated 6950 :mode planning :granularity nil :parent #186) #("In order to start up elasticsearch:\nPenguin - change user to \"elasticsearch\" and use the following command: \"env JAVA" 0 117 (:parent #189)) (subscript (:begin 7067 :end 7072 :use-brackets-p nil :contents-begin 7068 :contents-end 7072 :post-blank 0 :parent #189) #("HOME" 0 4 (:parent #193))) #("=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch\"\n" 0 60 (:parent #189)))) (headline (:raw-value "SystemD" :begin 7134 :end 7675 :pre-blank 1 :contents-begin 7146 :contents-end 7674 :robust-begin 7148 :robust-end 7672 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7134 :title (#("SystemD" 0 7 (:parent #187))) :parent #183 :cached t :org-element--cache-sync-key (1 . 7134) :granularity nil) (section (:begin 7146 :end 7675 :contents-begin 7146 :contents-end 7674 :robust-begin 7146 :robust-end 7672 :post-blank 1 :post-affiliated 7146 :mode section :granularity nil :parent #187) (paragraph (:begin 7146 :end 7206 :contents-begin 7146 :contents-end 7205 :post-blank 1 :post-affiliated 7146 :mode planning :granularity nil :parent #190) #("New server - as root run \"systemctl restart elasticsearch\"\n" 0 59 (:parent #193))) (src-block (:language nil :switches nil :parameters nil :begin 7206 :end 7674 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "tux01:/etc/systemd/system# cat elasticsearch.service\n[Unit]\nDescription=Run Elasticsearch\n\n[Service]\nExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch\nEnvironment=JAVA_HOME=/opt/jdk-9.0.4\nEnvironment=\"ES_JAVA_OPTS=-Xms1g -Xmx8g\"\nEnvironment=\"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin\"\nLimitNOFILE=65536\nStandardOutput=syslog\nStandardError=syslog\nUser=elasticsearch\n\n[Install]\nWantedBy=multi-user.target\n" :post-blank 0 :post-affiliated 7206 :mode nil :granularity nil :parent #190))))) (headline (:raw-value "Read more" :begin 7675 :end 7825 :pre-blank 1 :contents-begin 7688 :contents-end 7824 :robust-begin 7690 :robust-end 7822 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7675 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 7688 :end 7825 :contents-begin 7688 :contents-end 7824 :robust-begin 7688 :robust-end 7822 :post-blank 1 :post-affiliated 7688 :mode section :granularity nil :parent #184) (paragraph (:begin 7688 :end 7824 :contents-begin 7688 :contents-end 7824 :post-blank 0 :post-affiliated 7688 :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 7743 :end 7763 :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 "Trouble shooting" :begin 7825 :end 10276 :pre-blank 1 :contents-begin 7845 :contents-end 10274 :robust-begin 7847 :robust-end 10272 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7825 :title (#("Trouble shooting" 0 16 (:parent #185))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 7845 :end 8379 :pre-blank 1 :contents-begin 7885 :contents-end 8379 :robust-begin 7887 :robust-end 8377 :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 7845 :title (#("ImportError: No module named jinja2" 0 35 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 7885 :end 8379 :contents-begin 7885 :contents-end 8379 :robust-begin 7885 :robust-end 8377 :post-blank 0 :post-affiliated 7885 :mode section :granularity nil :parent #188) (paragraph (:begin 7885 :end 8120 :contents-begin 7885 :contents-end 8119 :post-blank 1 :post-affiliated 7885 :mode planning :granularity nil :parent #191) #("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 #194)) (subscript (:begin 8052 :end 8058 :use-brackets-p nil :contents-begin 8053 :contents-end 8057 :post-blank 1 :parent #194) #("PATH" 0 4 (:parent #198))) #("and R" 0 5 (:parent #194)) (subscript (:begin 8063 :end 8068 :use-brackets-p nil :contents-begin 8064 :contents-end 8068 :post-blank 0 :parent #194) #("LIBS" 0 4 (:parent #200))) (subscript (:begin 8068 :end 8074 :use-brackets-p nil :contents-begin 8069 :contents-end 8073 :post-blank 1 :parent #194) #("SITE" 0 4 (:parent #201))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #194))) (fixed-width (:begin 8120 :end 8151 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8120 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8151 :end 8167 :contents-begin 8151 :contents-end 8166 :post-blank 1 :post-affiliated 8151 :mode nil :granularity nil :parent #191) #("On one system:\n" 0 15 (:parent #196))) (fixed-width (:begin 8167 :end 8355 :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 8167 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8355 :end 8379 :contents-begin 8355 :contents-end 8379 :post-blank 0 :post-affiliated 8355 :mode nil :granularity nil :parent #191) #("and perhaps a few more.\n" 0 24 (:parent #198))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 8379 :end 8875 :pre-blank 1 :contents-begin 8488 :contents-end 8874 :robust-begin 8490 :robust-end 8872 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8379 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #189)) (subscript (:begin 8422 :end 8427 :use-brackets-p nil :contents-begin 8423 :contents-end 8427 :post-blank 0 :parent #189) #("data" 0 4 (:parent #231))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #189)) (subscript (:begin 8470 :end 8476 :use-brackets-p nil :contents-begin 8471 :contents-end 8476 :post-blank 0 :parent #189) #("files" 0 5 (:parent #233))) #("/genotype'" 0 10 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 8488 :end 8875 :contents-begin 8488 :contents-end 8874 :robust-begin 8488 :robust-end 8872 :post-blank 1 :post-affiliated 8488 :mode section :granularity nil :parent #189) (paragraph (:begin 8488 :end 8710 :contents-begin 8488 :contents-end 8709 :post-blank 1 :post-affiliated 8488 :mode planning :granularity nil :parent #192) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #195)) (subscript (:begin 8537 :end 8542 :use-brackets-p nil :contents-begin 8538 :contents-end 8542 :post-blank 0 :parent #195) #("data" 0 4 (:parent #199))) #(". 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 #195)) (subscript (:begin 8666 :end 8679 :use-brackets-p nil :contents-begin 8667 :contents-end 8678 :post-blank 1 :parent #195) #("settings.py" 0 11 (:parent #201))) #("(see above in\nthis document).\n" 0 30 (:parent #195))) (paragraph (:begin 8710 :end 8784 :contents-begin 8710 :contents-end 8783 :post-blank 1 :post-affiliated 8710 :mode nil :granularity nil :parent #192) #("You can use the GENENETWORK" 0 27 (:parent #196)) (subscript (:begin 8737 :end 8744 :use-brackets-p nil :contents-begin 8738 :contents-end 8743 :post-blank 1 :parent #196) #("FILES" 0 5 (:parent #200))) #("switch to set the datadir, for example\n" 0 39 (:parent #196))) (fixed-width (:begin 8784 :end 8874 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 8784 :mode nil :granularity nil :parent #192)))) (headline (:raw-value "Can't run a module" :begin 8875 :end 9109 :pre-blank 1 :contents-begin 8898 :contents-end 9109 :robust-begin 8900 :robust-end 9107 :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 8875 :title (#("Can't run a module" 0 18 (:parent #190))) :mode nil :granularity nil :parent #185) (section (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :robust-begin 8898 :robust-end 9107 :post-blank 0 :post-affiliated 8898 :mode section :granularity nil :parent #190) (paragraph (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :post-blank 0 :post-affiliated 8898 :mode planning :granularity nil :parent #193) #("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 #196))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 9109 :end 9610 :pre-blank 1 :contents-begin 9141 :contents-end 9609 :robust-begin 9143 :robust-end 9607 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9109 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #191))) :mode nil :granularity nil :parent #185) (section (:begin 9141 :end 9610 :contents-begin 9141 :contents-end 9609 :robust-begin 9141 :robust-end 9607 :post-blank 1 :post-affiliated 9141 :mode section :granularity nil :parent #191) (paragraph (:begin 9141 :end 9153 :contents-begin 9141 :contents-end 9152 :post-blank 1 :post-affiliated 9141 :mode planning :granularity nil :parent #194) #("This error\n" 0 11 (:parent #197))) (fixed-width (:begin 9153 :end 9233 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 9153 :mode nil :granularity nil :parent #194)) (paragraph (:begin 9233 :end 9364 :contents-begin 9233 :contents-end 9363 :post-blank 1 :post-affiliated 9233 :mode nil :granularity nil :parent #194) #("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 #199))) (paragraph (:begin 9364 :end 9609 :contents-begin 9364 :contents-end 9609 :post-blank 0 :post-affiliated 9364 :mode nil :granularity nil :parent #194) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #200)) (subscript (:begin 9427 :end 9432 :use-brackets-p nil :contents-begin 9428 :contents-end 9432 :post-blank 0 :parent #200) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 9432 :end 9437 :use-brackets-p nil :contents-begin 9433 :contents-end 9437 :post-blank 0 :parent #200) #("SITE" 0 4 (:parent #205))) #(". 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 #200))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 9610 :end 10276 :pre-blank 1 :contents-begin 9662 :contents-end 10274 :robust-begin 9664 :robust-end 10272 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9610 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #192))) :mode nil :granularity nil :parent #185) (section (:begin 9662 :end 10276 :contents-begin 9662 :contents-end 10274 :robust-begin 9662 :robust-end 10272 :post-blank 2 :post-affiliated 9662 :mode section :granularity nil :parent #192) (paragraph (:begin 9662 :end 9683 :contents-begin 9662 :contents-end 9682 :post-blank 1 :post-affiliated 9662 :mode planning :granularity nil :parent #195) #("The following error\n" 0 20 (:parent #198))) (fixed-width (:begin 9683 :end 9878 :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 9683 :mode nil :granularity nil :parent #195)) (paragraph (:begin 9878 :end 10036 :contents-begin 9878 :contents-end 10035 :post-blank 1 :post-affiliated 9878 :mode nil :granularity nil :parent #195) #("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 #200))) (fixed-width (:begin 10036 :end 10058 :value "mysql -h localhost" :post-blank 2 :post-affiliated 10036 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10058 :end 10115 :contents-begin 10058 :contents-end 10114 :post-blank 1 :post-affiliated 10058 :mode nil :granularity nil :parent #195) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #202))) (fixed-width (:begin 10115 :end 10137 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 10115 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10137 :end 10208 :contents-begin 10137 :contents-end 10207 :post-blank 1 :post-affiliated 10137 :mode nil :granularity nil :parent #195) #("if that works run genenetwork after setting SQL" 0 47 (:parent #204)) (subscript (:begin 10184 :end 10189 :use-brackets-p nil :contents-begin 10185 :contents-end 10188 :post-blank 1 :parent #204) #("URI" 0 3 (:parent #208))) #("to something like\n" 0 18 (:parent #204))) (fixed-width (:begin 10208 :end 10274 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 10208 :mode nil :granularity nil :parent #195))))) (headline (:raw-value "IRC session" :begin 10276 :end 14428 :pre-blank 1 :contents-begin 10291 :contents-end 14428 :robust-begin 10293 :robust-end 14426 :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 10276 :title (#("IRC session" 0 11 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 10291 :end 14428 :contents-begin 10291 :contents-end 14428 :robust-begin 10291 :robust-end 14426 :post-blank 0 :post-affiliated 10291 :mode section :granularity nil :parent #186) (paragraph (:begin 10291 :end 10400 :contents-begin 10291 :contents-end 10399 :post-blank 1 :post-affiliated 10291 :mode planning :granularity nil :parent #189) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #192))) (paragraph (:begin 10400 :end 10961 :contents-begin 10400 :contents-end 10960 :post-blank 1 :post-affiliated 10400 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 10407 :end 10411 :use-brackets-p nil :contents-begin 10408 :contents-end 10411 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\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 #193))) (paragraph (:begin 10961 :end 11051 :contents-begin 10961 :contents-end 11050 :post-blank 1 :post-affiliated 10961 :mode nil :granularity nil :parent #189) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 11051 :end 11196 :contents-begin 11051 :contents-end 11195 :post-blank 1 :post-affiliated 11051 :mode nil :granularity nil :parent #189) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 11081 :end 11089 :use-brackets-p nil :contents-begin 11082 :contents-end 11089 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 11089 :end 11094 :use-brackets-p nil :contents-begin 11090 :contents-end 11094 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 11196 :end 11492 :contents-begin 11196 :contents-end 11491 :post-blank 1 :post-affiliated 11196 :mode nil :granularity nil :parent #189) #("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 #196))) (paragraph (:begin 11492 :end 12685 :contents-begin 11492 :contents-end 12684 :post-blank 1 :post-affiliated 11492 :mode nil :granularity nil :parent #189) #(" 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 #197)) (subscript (:begin 12245 :end 12253 :use-brackets-p nil :contents-begin 12246 :contents-end 12253 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 12253 :end 12258 :use-brackets-p nil :contents-begin 12254 :contents-end 12258 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../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 #197))) (paragraph (:begin 12685 :end 12889 :contents-begin 12685 :contents-end 12888 :post-blank 1 :post-affiliated 12685 :mode nil :granularity nil :parent #189) #("/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 #198))) (paragraph (:begin 12889 :end 14428 :contents-begin 12889 :contents-end 14428 :post-blank 0 :post-affiliated 12889 :mode nil :granularity nil :parent #189) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 12937 :end 13846 :post-blank 0 :contents-begin 12938 :contents-end 13845 :parent #199) #("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 #203))) #(".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" 0 582 (:parent #199))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 268 :contents-begin 159 :contents-end 268 :checkbox nil :counter nil :structure ((121 1 "- " nil nil 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In this document we\nexplain the GeneNetwork version 2 (GN2) reproducible deployment system\nwhich is based on GNU Guix (see also " 0 130 (:parent #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 1557 :end 1631 :contents-begin 1619 :contents-end 1629 :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 1714 :end 2064 :contents-begin 1714 :contents-end 2063 :post-blank 1 :post-affiliated 1714 :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 1932 :end 2008 :contents-begin 1986 :contents-end 2005 :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 2012 :end 2061 :contents-begin 2051 :contents-end 2059 :post-blank 0 :parent #350) #("GNU Guix" 0 8 (:parent #356))) #(".\n" 0 2 (:parent #350))) (paragraph (:begin 2064 :end 2199 :contents-begin 2064 :contents-end 2199 :post-blank 0 :post-affiliated 2064 :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 2150 :end 2197 :contents-begin 2175 :contents-end 2195 :post-blank 0 :parent #351) #("GN2 Dependency Graph" 0 20 (:parent #355))) #(".\n" 0 2 (:parent #351))))) (headline (:raw-value "Install" :begin 2200 :end 3583 :pre-blank 1 :contents-begin 2211 :contents-end 3582 :robust-begin 2213 :robust-end 3580 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2200 :title (#("Install" 0 7 (:parent #344))) :mode nil :granularity nil :parent #338) (section (:begin 2211 :end 2575 :contents-begin 2211 :contents-end 2574 :robust-begin 2211 :robust-end 2572 :post-blank 1 :post-affiliated 2211 :mode section :granularity nil :parent #344) (paragraph (:begin 2211 :end 2574 :contents-begin 2211 :contents-end 2574 :post-blank 0 :post-affiliated 2211 :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 2575 :end 3228 :pre-blank 1 :contents-begin 2587 :contents-end 3227 :robust-begin 2589 :robust-end 3225 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2575 :title (#("Tarball" 0 7 (:parent #348))) :mode nil :granularity nil :parent #344) (section (:begin 2587 :end 3228 :contents-begin 2587 :contents-end 3227 :robust-begin 2587 :robust-end 3225 :post-blank 1 :post-affiliated 2587 :mode section :granularity nil :parent #348) (paragraph (:begin 2587 :end 2734 :contents-begin 2587 :contents-end 2733 :post-blank 1 :post-affiliated 2587 :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 2620 :end 2677 :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 2734 :end 2836 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2734 :mode nil :granularity nil :parent #351)) (paragraph (:begin 2836 :end 2884 :contents-begin 2836 :contents-end 2883 :post-blank 1 :post-affiliated 2836 :mode nil :granularity nil :parent #351) #("Now you shoud be able to start the server with\n" 0 47 (:parent #356))) (fixed-width (:begin 2884 :end 2922 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2884 :mode nil :granularity nil :parent #351)) (paragraph (:begin 2922 :end 3049 :contents-begin 2922 :contents-end 3048 :post-blank 1 :post-affiliated 2922 :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 2963 :end 3002 :contents-begin 2984 :contents-end 3000 :post-blank 0 :parent #358) #("Run MySQL server" 0 16 (:parent #362))) #("\nand set SQL" 0 12 (:parent #358)) (subscript (:begin 3014 :end 3019 :use-brackets-p nil :contents-begin 3015 :contents-end 3018 :post-blank 1 :parent #358) #("URI" 0 3 (:parent #364))) #("to point at it. For example:\n" 0 29 (:parent #358))) (fixed-width (:begin 3049 :end 3116 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 3049 :mode nil :granularity nil :parent #351)) (paragraph (:begin 3116 :end 3227 :contents-begin 3116 :contents-end 3227 :post-blank 0 :post-affiliated 3116 :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 3125 :end 3225 :contents-begin 3176 :contents-end 3223 :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 3228 :end 3437 :pre-blank 1 :contents-begin 3239 :contents-end 3436 :robust-begin 3241 :robust-end 3434 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3228 :title (#("Docker" 0 6 (:parent #349))) :mode nil :granularity nil :parent #344) (section (:begin 3239 :end 3437 :contents-begin 3239 :contents-end 3436 :robust-begin 3239 :robust-end 3434 :post-blank 1 :post-affiliated 3239 :mode section :granularity nil :parent #349) (paragraph (:begin 3239 :end 3436 :contents-begin 3239 :contents-end 3436 :post-blank 0 :post-affiliated 3239 :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 3280 :end 3322 :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 3359 :end 3434 :contents-begin 3421 :contents-end 3432 :post-blank 0 :parent #355) #("Docker load" 0 11 (:parent #361))) #(".\n" 0 2 (:parent #355))))) (headline (:raw-value "With source" :begin 3437 :end 3583 :pre-blank 1 :contents-begin 3453 :contents-end 3582 :robust-begin 3455 :robust-end 3580 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3437 :title (#("With source" 0 11 (:parent #350))) :mode nil :granularity nil :parent #344) (section (:begin 3453 :end 3583 :contents-begin 3453 :contents-end 3582 :robust-begin 3453 :robust-end 3580 :post-blank 1 :post-affiliated 3453 :mode section :granularity nil :parent #350) (paragraph (:begin 3453 :end 3582 :contents-begin 3453 :contents-end 3582 :post-blank 0 :post-affiliated 3453 :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 3539 :end 3580 :contents-begin 3561 :contents-end 3578 :post-blank 0 :parent #356) #("Source deployment" 0 17 (:parent #360))) #(".\n" 0 2 (:parent #356)))))) (headline (:raw-value "Running GN2" :begin 3583 :end 4064 :pre-blank 1 :contents-begin 3598 :contents-end 4063 :robust-begin 3600 :robust-end 4061 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3583 :title (#("Running GN2" 0 11 (:parent #345))) :mode nil :granularity nil :parent #338) (section (:begin 3598 :end 4064 :contents-begin 3598 :contents-end 4063 :robust-begin 3598 :robust-end 4061 :post-blank 1 :post-affiliated 3598 :mode section :granularity nil :parent #345) (paragraph (:begin 3598 :end 3793 :contents-begin 3598 :contents-end 3792 :post-blank 1 :post-affiliated 3598 :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 3651 :end 3702 :contents-begin 3681 :contents-end 3700 :post-blank 0 :parent #351) #("default" 0 7 (:parent #355)) (subscript (:begin 3688 :end 3700 :use-brackets-p nil :contents-begin 3689 :contents-end 3700 :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 3793 :end 3823 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3793 :mode nil :granularity nil :parent #348)) (paragraph (:begin 3823 :end 3901 :contents-begin 3823 :contents-end 3900 :post-blank 1 :post-affiliated 3823 :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 3901 :end 3984 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3901 :mode nil :granularity nil :parent #348)) (paragraph (:begin 3984 :end 4063 :contents-begin 3984 :contents-end 4063 :post-blank 0 :post-affiliated 3984 :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 4064 :end 6699 :pre-blank 0 :contents-begin 4083 :contents-end 6698 :robust-begin 4085 :robust-end 6696 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4064 :title (#("Run MySQL server" 0 16 (:parent #346))) :mode nil :granularity nil :parent #338) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 4083 :end 5167 :pre-blank 1 :contents-begin 4115 :contents-end 5166 :robust-begin 4117 :robust-end 5164 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4083 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #349))) :mode section :granularity nil :parent #346) (section (:begin 4115 :end 5167 :contents-begin 4115 :contents-end 5166 :robust-begin 4115 :robust-end 5164 :post-blank 1 :post-affiliated 4115 :mode section :granularity nil :parent #349) (paragraph (:begin 4115 :end 4250 :contents-begin 4115 :contents-end 4249 :post-blank 1 :post-affiliated 4115 :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 4250 :end 4277 :contents-begin 4250 :contents-end 4276 :post-blank 1 :post-affiliated 4250 :mode nil :granularity nil :parent #352) #("As root configure and run\n" 0 26 (:parent #356))) (src-block (:language "bash" :switches nil :parameters nil :begin 4277 :end 4535 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mysql && addgroup mysql\nmysqld --datadir=/var/mysql --initialize-insecure\nmkdir -p /var/run/mysqld\nchown mysql.mysql ~/mysql /var/run/mysqld\nmysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 4277 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4535 :end 4583 :contents-begin 4535 :contents-end 4582 :post-blank 1 :post-affiliated 4535 :mode nil :granularity nil :parent #352) #("If you want to run as root you may have to set\n" 0 47 (:parent #358))) (fixed-width (:begin 4583 :end 4621 :value "/etc/my.cnf\n[mysqld]\nuser=root" :post-blank 2 :post-affiliated 4583 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4621 :end 4690 :contents-begin 4621 :contents-end 4689 :post-blank 1 :post-affiliated 4621 :mode nil :granularity nil :parent #352) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #360))) (fixed-width (:begin 4690 :end 4799 :value "mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log" :post-blank 2 :post-affiliated 4690 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4799 :end 4875 :contents-begin 4799 :contents-end 4874 :post-blank 1 :post-affiliated 4799 :mode nil :granularity nil :parent #352) #("Other tips are that Guix installs mysqld in your profile, so this may work\n" 0 75 (:parent #362))) (fixed-width (:begin 4875 :end 4979 :value "/home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql" :post-blank 2 :post-affiliated 4875 :mode nil :granularity nil :parent #352)) (paragraph (:begin 4979 :end 5006 :contents-begin 4979 :contents-end 5005 :post-blank 1 :post-affiliated 4979 :mode nil :granularity nil :parent #352) #("When you get errors like:\n" 0 26 (:parent #364))) (fixed-width (:begin 5006 :end 5118 :value "qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 5006 :mode nil :granularity nil :parent #352)) (paragraph (:begin 5118 :end 5139 :contents-begin 5118 :contents-end 5138 :post-blank 1 :post-affiliated 5118 :mode nil :granularity nil :parent #352) #("you may need to set\n" 0 20 (:parent #366))) (fixed-width (:begin 5139 :end 5166 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 5139 :mode nil :granularity nil :parent #352)))) (headline (:raw-value "Load the small database in MySQL" :begin 5167 :end 6699 :pre-blank 1 :contents-begin 5204 :contents-end 6698 :robust-begin 5206 :robust-end 6696 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5167 :title (#("Load the small database in MySQL" 0 32 (:parent #350))) :mode nil :granularity nil :parent #346) (section (:begin 5204 :end 6699 :contents-begin 5204 :contents-end 6698 :robust-begin 5204 :robust-end 6696 :post-blank 1 :post-affiliated 5204 :mode section :granularity nil :parent #350) (paragraph (:begin 5204 :end 5511 :contents-begin 5204 :contents-end 5510 :post-blank 1 :post-affiliated 5204 :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 5367 :end 5374 :use-brackets-p nil :contents-begin 5368 :contents-end 5374 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #360))) (subscript (:begin 5374 :end 5376 :use-brackets-p nil :contents-begin 5375 :contents-end 5376 :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 5452 :end 5459 :use-brackets-p nil :contents-begin 5453 :contents-end 5459 :post-blank 0 :parent #356) #("webqtl" 0 6 (:parent #363))) (subscript (:begin 5459 :end 5465 :use-brackets-p nil :contents-begin 5460 :contents-end 5465 :post-blank 0 :parent #356) #("plant" 0 5 (:parent #364))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #356))) (paragraph (:begin 5511 :end 5539 :contents-begin 5511 :contents-end 5538 :post-blank 1 :post-affiliated 5511 :mode nil :granularity nil :parent #353) #("Download one database from\n" 0 27 (:parent #357))) (paragraph (:begin 5539 :end 5587 :contents-begin 5539 :contents-end 5586 :post-blank 1 :post-affiliated 5539 :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 5539 :end 5585 :contents-begin nil :contents-end nil :post-blank 0 :parent #358)) #("\n" 0 1 (:parent #358))) (paragraph (:begin 5587 :end 5646 :contents-begin 5587 :contents-end 5645 :post-blank 1 :post-affiliated 5587 :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 5587 :end 5644 :contents-begin nil :contents-end nil :post-blank 0 :parent #359)) #("\n" 0 1 (:parent #359))) (paragraph (:begin 5646 :end 5665 :contents-begin 5646 :contents-end 5664 :post-blank 1 :post-affiliated 5646 :mode nil :granularity nil :parent #353) #("Check the md5sum.\n" 0 18 (:parent #360))) (paragraph (:begin 5665 :end 5736 :contents-begin 5665 :contents-end 5735 :post-blank 1 :post-affiliated 5665 :mode nil :granularity nil :parent #353) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #361))) (fixed-width (:begin 5736 :end 5837 :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 5736 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5837 :end 5884 :contents-begin 5837 :contents-end 5883 :post-blank 1 :post-affiliated 5837 :mode nil :granularity nil :parent #353) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #363))) (fixed-width (:begin 5884 :end 5901 :value "myslq -u root" :post-blank 2 :post-affiliated 5884 :mode nil :granularity nil :parent #353)) (paragraph (:begin 5901 :end 5906 :contents-begin 5901 :contents-end 5905 :post-blank 1 :post-affiliated 5901 :mode nil :granularity nil :parent #353) #("and\n" 0 4 (:parent #365))) (fixed-width (:begin 5906 :end 6132 :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 5906 :mode nil :granularity nil :parent #353)) (paragraph (:begin 6132 :end 6197 :contents-begin 6132 :contents-end 6196 :post-blank 1 :post-affiliated 6132 :mode nil :granularity nil :parent #353) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #367))) (fixed-width (:begin 6197 :end 6296 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 6197 :mode nil :granularity nil :parent #353)) (paragraph (:begin 6296 :end 6403 :contents-begin 6296 :contents-end 6402 :post-blank 1 :post-affiliated 6296 :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 6403 :end 6566 :contents-begin 6403 :contents-end 6565 :post-blank 1 :post-affiliated 6403 :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 6566 :end 6698 :contents-begin 6566 :contents-end 6698 :post-blank 0 :post-affiliated 6566 :mode nil :granularity nil :parent #353) #("Note for the plant database you can rename it to db" 0 51 (:parent #371)) (subscript (:begin 6617 :end 6624 :use-brackets-p nil :contents-begin 6618 :contents-end 6624 :post-blank 0 :parent #371) #("webqtl" 0 6 (:parent #375))) (subscript (:begin 6624 :end 6626 :use-brackets-p nil :contents-begin 6625 :contents-end 6626 :post-blank 0 :parent #371) #("s" 0 1 (:parent #376))) #(", or\nchange the settings in etc/default" 0 39 (:parent #371)) (subscript (:begin 6665 :end 6678 :use-brackets-p nil :contents-begin 6666 :contents-end 6677 :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 6699 :end 6863 :pre-blank 1 :contents-begin 6723 :contents-end 6862 :robust-begin 6725 :robust-end 6860 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6699 :title (#("GN2 Dependency Graph" 0 20 (:parent #347))) :mode nil :granularity nil :parent #338) (section (:begin 6723 :end 6863 :contents-begin 6723 :contents-end 6862 :robust-begin 6723 :robust-end 6860 :post-blank 1 :post-affiliated 6723 :mode section :granularity nil :parent #347) (paragraph (:begin 6723 :end 6784 :contents-begin 6723 :contents-end 6783 :post-blank 1 :post-affiliated 6723 :mode planning :granularity nil :parent #350) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #353))) (paragraph (:begin 6784 :end 6862 :contents-begin 6814 :contents-end 6862 :post-blank 0 :post-affiliated 6814 :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 6814 :end 6861 :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 6863 :end 6925 :pre-blank 1 :contents-begin 6899 :contents-end 6924 :robust-begin 6901 :robust-end 6922 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6863 :title (#("Working with the GN2 source code" 0 32 (:parent #348))) :mode nil :granularity nil :parent #338) (section (:begin 6899 :end 6925 :contents-begin 6899 :contents-end 6924 :robust-begin 6899 :robust-end 6922 :post-blank 1 :post-affiliated 6899 :mode section :granularity nil :parent #348) (paragraph (:begin 6899 :end 6924 :contents-begin 6899 :contents-end 6924 :post-blank 0 :post-affiliated 6899 :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 6903 :end 6922 :contents-begin nil :contents-end nil :post-blank 0 :parent #354)) #(".\n" 0 2 (:parent #354))))) (headline (:raw-value "Running ElasticSearch" :begin 6925 :end 7675 :pre-blank 1 :contents-begin 6950 :contents-end 7674 :robust-begin 6952 :robust-end 7672 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6925 :title (#("Running ElasticSearch" 0 21 (:parent #349))) :parent #338 :cached t :granularity nil) (section (:begin 6950 :end 7134 :contents-begin 6950 :contents-end 7132 :robust-begin 6950 :robust-end 7130 :post-blank 2 :post-affiliated 6950 :mode section :granularity nil :parent #349) (paragraph (:begin 6950 :end 7132 :contents-begin 6950 :contents-end 7132 :post-blank 0 :post-affiliated 6950 :mode planning :granularity nil :parent #352) #("In order to start up elasticsearch:\nPenguin - change user to \"elasticsearch\" and use the following command: \"env JAVA" 0 117 (:parent #355)) (subscript (:begin 7067 :end 7072 :use-brackets-p nil :contents-begin 7068 :contents-end 7072 :post-blank 0 :parent #355) #("HOME" 0 4 (:parent #359))) #("=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch\"\n" 0 60 (:parent #355)))) (headline (:raw-value "SystemD" :begin 7134 :end 7675 :pre-blank 1 :contents-begin 7146 :contents-end 7674 :robust-begin 7148 :robust-end 7672 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7134 :title (#("SystemD" 0 7 (:parent #353))) :parent #349 :cached t :org-element--cache-sync-key (1 . 7134) :granularity nil) (section (:begin 7146 :end 7675 :contents-begin 7146 :contents-end 7674 :robust-begin 7146 :robust-end 7672 :post-blank 1 :post-affiliated 7146 :mode section :granularity nil :parent #353) (paragraph (:begin 7146 :end 7206 :contents-begin 7146 :contents-end 7205 :post-blank 1 :post-affiliated 7146 :mode planning :granularity nil :parent #356) #("New server - as root run \"systemctl restart elasticsearch\"\n" 0 59 (:parent #359))) (src-block (:language nil :switches nil :parameters nil :begin 7206 :end 7674 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "tux01:/etc/systemd/system# cat elasticsearch.service\n[Unit]\nDescription=Run Elasticsearch\n\n[Service]\nExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch\nEnvironment=JAVA_HOME=/opt/jdk-9.0.4\nEnvironment=\"ES_JAVA_OPTS=-Xms1g -Xmx8g\"\nEnvironment=\"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin\"\nLimitNOFILE=65536\nStandardOutput=syslog\nStandardError=syslog\nUser=elasticsearch\n\n[Install]\nWantedBy=multi-user.target\n" :post-blank 0 :post-affiliated 7206 :mode nil :granularity nil :parent #356))))) (headline (:raw-value "Read more" :begin 7675 :end 7825 :pre-blank 1 :contents-begin 7688 :contents-end 7824 :robust-begin 7690 :robust-end 7822 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7675 :title (#("Read more" 0 9 (:parent #350))) :mode nil :granularity nil :parent #338) (section (:begin 7688 :end 7825 :contents-begin 7688 :contents-end 7824 :robust-begin 7688 :robust-end 7822 :post-blank 1 :post-affiliated 7688 :mode section :granularity nil :parent #350) (paragraph (:begin 7688 :end 7824 :contents-begin 7688 :contents-end 7824 :post-blank 0 :post-affiliated 7688 :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 7743 :end 7763 :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 "Trouble shooting" :begin 7825 :end 10276 :pre-blank 1 :contents-begin 7845 :contents-end 10274 :robust-begin 7847 :robust-end 10272 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7825 :title (#("Trouble shooting" 0 16 (:parent #351))) :mode nil :granularity nil :parent #338) (headline (:raw-value "ImportError: No module named jinja2" :begin 7845 :end 8379 :pre-blank 1 :contents-begin 7885 :contents-end 8379 :robust-begin 7887 :robust-end 8377 :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 7845 :title (#("ImportError: No module named jinja2" 0 35 (:parent #354))) :mode section :granularity nil :parent #351) (section (:begin 7885 :end 8379 :contents-begin 7885 :contents-end 8379 :robust-begin 7885 :robust-end 8377 :post-blank 0 :post-affiliated 7885 :mode section :granularity nil :parent #354) (paragraph (:begin 7885 :end 8120 :contents-begin 7885 :contents-end 8119 :post-blank 1 :post-affiliated 7885 :mode planning :granularity nil :parent #357) #("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 #360)) (subscript (:begin 8052 :end 8058 :use-brackets-p nil :contents-begin 8053 :contents-end 8057 :post-blank 1 :parent #360) #("PATH" 0 4 (:parent #364))) #("and R" 0 5 (:parent #360)) (subscript (:begin 8063 :end 8068 :use-brackets-p nil :contents-begin 8064 :contents-end 8068 :post-blank 0 :parent #360) #("LIBS" 0 4 (:parent #366))) (subscript (:begin 8068 :end 8074 :use-brackets-p nil :contents-begin 8069 :contents-end 8073 :post-blank 1 :parent #360) #("SITE" 0 4 (:parent #367))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #360))) (fixed-width (:begin 8120 :end 8151 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8120 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8151 :end 8167 :contents-begin 8151 :contents-end 8166 :post-blank 1 :post-affiliated 8151 :mode nil :granularity nil :parent #357) #("On one system:\n" 0 15 (:parent #362))) (fixed-width (:begin 8167 :end 8355 :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 8167 :mode nil :granularity nil :parent #357)) (paragraph (:begin 8355 :end 8379 :contents-begin 8355 :contents-end 8379 :post-blank 0 :post-affiliated 8355 :mode nil :granularity nil :parent #357) #("and perhaps a few more.\n" 0 24 (:parent #364))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 8379 :end 8875 :pre-blank 1 :contents-begin 8488 :contents-end 8874 :robust-begin 8490 :robust-end 8872 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8379 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #355)) (subscript (:begin 8422 :end 8427 :use-brackets-p nil :contents-begin 8423 :contents-end 8427 :post-blank 0 :parent #355) #("data" 0 4 (:parent #397))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #355)) (subscript (:begin 8470 :end 8476 :use-brackets-p nil :contents-begin 8471 :contents-end 8476 :post-blank 0 :parent #355) #("files" 0 5 (:parent #399))) #("/genotype'" 0 10 (:parent #355))) :mode nil :granularity nil :parent #351) (section (:begin 8488 :end 8875 :contents-begin 8488 :contents-end 8874 :robust-begin 8488 :robust-end 8872 :post-blank 1 :post-affiliated 8488 :mode section :granularity nil :parent #355) (paragraph (:begin 8488 :end 8710 :contents-begin 8488 :contents-end 8709 :post-blank 1 :post-affiliated 8488 :mode planning :granularity nil :parent #358) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #361)) (subscript (:begin 8537 :end 8542 :use-brackets-p nil :contents-begin 8538 :contents-end 8542 :post-blank 0 :parent #361) #("data" 0 4 (:parent #365))) #(". 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 #361)) (subscript (:begin 8666 :end 8679 :use-brackets-p nil :contents-begin 8667 :contents-end 8678 :post-blank 1 :parent #361) #("settings.py" 0 11 (:parent #367))) #("(see above in\nthis document).\n" 0 30 (:parent #361))) (paragraph (:begin 8710 :end 8784 :contents-begin 8710 :contents-end 8783 :post-blank 1 :post-affiliated 8710 :mode nil :granularity nil :parent #358) #("You can use the GENENETWORK" 0 27 (:parent #362)) (subscript (:begin 8737 :end 8744 :use-brackets-p nil :contents-begin 8738 :contents-end 8743 :post-blank 1 :parent #362) #("FILES" 0 5 (:parent #366))) #("switch to set the datadir, for example\n" 0 39 (:parent #362))) (fixed-width (:begin 8784 :end 8874 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 8784 :mode nil :granularity nil :parent #358)))) (headline (:raw-value "Can't run a module" :begin 8875 :end 9109 :pre-blank 1 :contents-begin 8898 :contents-end 9109 :robust-begin 8900 :robust-end 9107 :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 8875 :title (#("Can't run a module" 0 18 (:parent #356))) :mode nil :granularity nil :parent #351) (section (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :robust-begin 8898 :robust-end 9107 :post-blank 0 :post-affiliated 8898 :mode section :granularity nil :parent #356) (paragraph (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :post-blank 0 :post-affiliated 8898 :mode planning :granularity nil :parent #359) #("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 #362))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 9109 :end 9610 :pre-blank 1 :contents-begin 9141 :contents-end 9609 :robust-begin 9143 :robust-end 9607 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9109 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #357))) :mode nil :granularity nil :parent #351) (section (:begin 9141 :end 9610 :contents-begin 9141 :contents-end 9609 :robust-begin 9141 :robust-end 9607 :post-blank 1 :post-affiliated 9141 :mode section :granularity nil :parent #357) (paragraph (:begin 9141 :end 9153 :contents-begin 9141 :contents-end 9152 :post-blank 1 :post-affiliated 9141 :mode planning :granularity nil :parent #360) #("This error\n" 0 11 (:parent #363))) (fixed-width (:begin 9153 :end 9233 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 9153 :mode nil :granularity nil :parent #360)) (paragraph (:begin 9233 :end 9364 :contents-begin 9233 :contents-end 9363 :post-blank 1 :post-affiliated 9233 :mode nil :granularity nil :parent #360) #("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 #365))) (paragraph (:begin 9364 :end 9609 :contents-begin 9364 :contents-end 9609 :post-blank 0 :post-affiliated 9364 :mode nil :granularity nil :parent #360) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #366)) (subscript (:begin 9427 :end 9432 :use-brackets-p nil :contents-begin 9428 :contents-end 9432 :post-blank 0 :parent #366) #("LIBS" 0 4 (:parent #370))) (subscript (:begin 9432 :end 9437 :use-brackets-p nil :contents-begin 9433 :contents-end 9437 :post-blank 0 :parent #366) #("SITE" 0 4 (:parent #371))) #(". 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 #366))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 9610 :end 10276 :pre-blank 1 :contents-begin 9662 :contents-end 10274 :robust-begin 9664 :robust-end 10272 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9610 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #358))) :mode nil :granularity nil :parent #351) (section (:begin 9662 :end 10276 :contents-begin 9662 :contents-end 10274 :robust-begin 9662 :robust-end 10272 :post-blank 2 :post-affiliated 9662 :mode section :granularity nil :parent #358) (paragraph (:begin 9662 :end 9683 :contents-begin 9662 :contents-end 9682 :post-blank 1 :post-affiliated 9662 :mode planning :granularity nil :parent #361) #("The following error\n" 0 20 (:parent #364))) (fixed-width (:begin 9683 :end 9878 :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 9683 :mode nil :granularity nil :parent #361)) (paragraph (:begin 9878 :end 10036 :contents-begin 9878 :contents-end 10035 :post-blank 1 :post-affiliated 9878 :mode nil :granularity nil :parent #361) #("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 #366))) (fixed-width (:begin 10036 :end 10058 :value "mysql -h localhost" :post-blank 2 :post-affiliated 10036 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10058 :end 10115 :contents-begin 10058 :contents-end 10114 :post-blank 1 :post-affiliated 10058 :mode nil :granularity nil :parent #361) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #368))) (fixed-width (:begin 10115 :end 10137 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 10115 :mode nil :granularity nil :parent #361)) (paragraph (:begin 10137 :end 10208 :contents-begin 10137 :contents-end 10207 :post-blank 1 :post-affiliated 10137 :mode nil :granularity nil :parent #361) #("if that works run genenetwork after setting SQL" 0 47 (:parent #370)) (subscript (:begin 10184 :end 10189 :use-brackets-p nil :contents-begin 10185 :contents-end 10188 :post-blank 1 :parent #370) #("URI" 0 3 (:parent #374))) #("to something like\n" 0 18 (:parent #370))) (fixed-width (:begin 10208 :end 10274 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 10208 :mode nil :granularity nil :parent #361))))) (headline (:raw-value "IRC session" :begin 10276 :end 14428 :pre-blank 1 :contents-begin 10291 :contents-end 14428 :robust-begin 10293 :robust-end 14426 :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 10276 :title (#("IRC session" 0 11 (:parent #352))) :mode nil :granularity nil :parent #338) (section (:begin 10291 :end 14428 :contents-begin 10291 :contents-end 14428 :robust-begin 10291 :robust-end 14426 :post-blank 0 :post-affiliated 10291 :mode section :granularity nil :parent #352) (paragraph (:begin 10291 :end 10400 :contents-begin 10291 :contents-end 10399 :post-blank 1 :post-affiliated 10291 :mode planning :granularity nil :parent #355) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #358))) (paragraph (:begin 10400 :end 10961 :contents-begin 10400 :contents-end 10960 :post-blank 1 :post-affiliated 10400 :mode nil :granularity nil :parent #355) #("#+begin" 0 7 (:parent #359)) (subscript (:begin 10407 :end 10411 :use-brackets-p nil :contents-begin 10408 :contents-end 10411 :post-blank 0 :parent #359) #("src" 0 3 (:parent #363))) #("\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 #359))) (paragraph (:begin 10961 :end 11051 :contents-begin 10961 :contents-end 11050 :post-blank 1 :post-affiliated 10961 :mode nil :granularity nil :parent #355) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #360))) (paragraph (:begin 11051 :end 11196 :contents-begin 11051 :contents-end 11195 :post-blank 1 :post-affiliated 11051 :mode nil :granularity nil :parent #355) #(" yes\n env GUIX" 0 30 (:parent #361)) (subscript (:begin 11081 :end 11089 :use-brackets-p nil :contents-begin 11082 :contents-end 11089 :post-blank 0 :parent #361) #("PACKAGE" 0 7 (:parent #365))) (subscript (:begin 11089 :end 11094 :use-brackets-p nil :contents-begin 11090 :contents-end 11094 :post-blank 0 :parent #361) #("PATH" 0 4 (:parent #366))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #361))) (paragraph (:begin 11196 :end 11492 :contents-begin 11196 :contents-end 11491 :post-blank 1 :post-affiliated 11196 :mode nil :granularity nil :parent #355) #("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 #362))) (paragraph (:begin 11492 :end 12685 :contents-begin 11492 :contents-end 12684 :post-blank 1 :post-affiliated 11492 :mode nil :granularity nil :parent #355) #(" 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 #363)) (subscript (:begin 12245 :end 12253 :use-brackets-p nil :contents-begin 12246 :contents-end 12253 :post-blank 0 :parent #363) #("PACKAGE" 0 7 (:parent #367))) (subscript (:begin 12253 :end 12258 :use-brackets-p nil :contents-begin 12254 :contents-end 12258 :post-blank 0 :parent #363) #("PATH" 0 4 (:parent #368))) #("=../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 #363))) (paragraph (:begin 12685 :end 12889 :contents-begin 12685 :contents-end 12888 :post-blank 1 :post-affiliated 12685 :mode nil :granularity nil :parent #355) #("/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 #364))) (paragraph (:begin 12889 :end 14428 :contents-begin 12889 :contents-end 14428 :post-blank 0 :post-affiliated 12889 :mode nil :granularity nil :parent #355) #(" which should have the same HASH values " 0 48 (:parent #365)) (italic (:begin 12937 :end 13846 :post-blank 0 :contents-begin 12938 :contents-end 13845 :parent #365) #("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 #369))) #(".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" 0 582 (:parent #365)))))) :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 1557 :end 1631 :contents-begin 1619 :contents-end 1629 :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 1714 :end 2064 :contents-begin 1714 :contents-end 2063 :post-blank 1 :post-affiliated 1714 :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 1932 :end 2008 :contents-begin 1986 :contents-end 2005 :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 2012 :end 2061 :contents-begin 2051 :contents-end 2059 :post-blank 0 :parent #184) #("GNU Guix" 0 8 (:parent #190))) #(".\n" 0 2 (:parent #184))) (paragraph (:begin 2064 :end 2199 :contents-begin 2064 :contents-end 2199 :post-blank 0 :post-affiliated 2064 :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 2150 :end 2197 :contents-begin 2175 :contents-end 2195 :post-blank 0 :parent #185) #("GN2 Dependency Graph" 0 20 (:parent #189))) #(".\n" 0 2 (:parent #185))))) (headline (:raw-value "Install" :begin 2200 :end 3583 :pre-blank 1 :contents-begin 2211 :contents-end 3582 :robust-begin 2213 :robust-end 3580 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2200 :title (#("Install" 0 7 (:parent #178))) :mode nil :granularity nil :parent #172) (section (:begin 2211 :end 2575 :contents-begin 2211 :contents-end 2574 :robust-begin 2211 :robust-end 2572 :post-blank 1 :post-affiliated 2211 :mode section :granularity nil :parent #178) (paragraph (:begin 2211 :end 2574 :contents-begin 2211 :contents-end 2574 :post-blank 0 :post-affiliated 2211 :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 2575 :end 3228 :pre-blank 1 :contents-begin 2587 :contents-end 3227 :robust-begin 2589 :robust-end 3225 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2575 :title (#("Tarball" 0 7 (:parent #182))) :mode nil :granularity nil :parent #178) (section (:begin 2587 :end 3228 :contents-begin 2587 :contents-end 3227 :robust-begin 2587 :robust-end 3225 :post-blank 1 :post-affiliated 2587 :mode section :granularity nil :parent #182) (paragraph (:begin 2587 :end 2734 :contents-begin 2587 :contents-end 2733 :post-blank 1 :post-affiliated 2587 :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 2620 :end 2677 :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 2734 :end 2836 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2734 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2836 :end 2884 :contents-begin 2836 :contents-end 2883 :post-blank 1 :post-affiliated 2836 :mode nil :granularity nil :parent #185) #("Now you shoud be able to start the server with\n" 0 47 (:parent #190))) (fixed-width (:begin 2884 :end 2922 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2884 :mode nil :granularity nil :parent #185)) (paragraph (:begin 2922 :end 3049 :contents-begin 2922 :contents-end 3048 :post-blank 1 :post-affiliated 2922 :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 2963 :end 3002 :contents-begin 2984 :contents-end 3000 :post-blank 0 :parent #192) #("Run MySQL server" 0 16 (:parent #196))) #("\nand set SQL" 0 12 (:parent #192)) (subscript (:begin 3014 :end 3019 :use-brackets-p nil :contents-begin 3015 :contents-end 3018 :post-blank 1 :parent #192) #("URI" 0 3 (:parent #198))) #("to point at it. For example:\n" 0 29 (:parent #192))) (fixed-width (:begin 3049 :end 3116 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 3049 :mode nil :granularity nil :parent #185)) (paragraph (:begin 3116 :end 3227 :contents-begin 3116 :contents-end 3227 :post-blank 0 :post-affiliated 3116 :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 3125 :end 3225 :contents-begin 3176 :contents-end 3223 :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 3228 :end 3437 :pre-blank 1 :contents-begin 3239 :contents-end 3436 :robust-begin 3241 :robust-end 3434 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3228 :title (#("Docker" 0 6 (:parent #183))) :mode nil :granularity nil :parent #178) (section (:begin 3239 :end 3437 :contents-begin 3239 :contents-end 3436 :robust-begin 3239 :robust-end 3434 :post-blank 1 :post-affiliated 3239 :mode section :granularity nil :parent #183) (paragraph (:begin 3239 :end 3436 :contents-begin 3239 :contents-end 3436 :post-blank 0 :post-affiliated 3239 :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 3280 :end 3322 :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 3359 :end 3434 :contents-begin 3421 :contents-end 3432 :post-blank 0 :parent #189) #("Docker load" 0 11 (:parent #195))) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "With source" :begin 3437 :end 3583 :pre-blank 1 :contents-begin 3453 :contents-end 3582 :robust-begin 3455 :robust-end 3580 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3437 :title (#("With source" 0 11 (:parent #184))) :mode nil :granularity nil :parent #178) (section (:begin 3453 :end 3583 :contents-begin 3453 :contents-end 3582 :robust-begin 3453 :robust-end 3580 :post-blank 1 :post-affiliated 3453 :mode section :granularity nil :parent #184) (paragraph (:begin 3453 :end 3582 :contents-begin 3453 :contents-end 3582 :post-blank 0 :post-affiliated 3453 :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 3539 :end 3580 :contents-begin 3561 :contents-end 3578 :post-blank 0 :parent #190) #("Source deployment" 0 17 (:parent #194))) #(".\n" 0 2 (:parent #190)))))) (headline (:raw-value "Running GN2" :begin 3583 :end 4064 :pre-blank 1 :contents-begin 3598 :contents-end 4063 :robust-begin 3600 :robust-end 4061 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3583 :title (#("Running GN2" 0 11 (:parent #179))) :mode nil :granularity nil :parent #172) (section (:begin 3598 :end 4064 :contents-begin 3598 :contents-end 4063 :robust-begin 3598 :robust-end 4061 :post-blank 1 :post-affiliated 3598 :mode section :granularity nil :parent #179) (paragraph (:begin 3598 :end 3793 :contents-begin 3598 :contents-end 3792 :post-blank 1 :post-affiliated 3598 :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 3651 :end 3702 :contents-begin 3681 :contents-end 3700 :post-blank 0 :parent #185) #("default" 0 7 (:parent #189)) (subscript (:begin 3688 :end 3700 :use-brackets-p nil :contents-begin 3689 :contents-end 3700 :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 3793 :end 3823 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3793 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3823 :end 3901 :contents-begin 3823 :contents-end 3900 :post-blank 1 :post-affiliated 3823 :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 3901 :end 3984 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3901 :mode nil :granularity nil :parent #182)) (paragraph (:begin 3984 :end 4063 :contents-begin 3984 :contents-end 4063 :post-blank 0 :post-affiliated 3984 :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 4064 :end 6699 :pre-blank 0 :contents-begin 4083 :contents-end 6698 :robust-begin 4085 :robust-end 6696 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4064 :title (#("Run MySQL server" 0 16 (:parent #180))) :mode nil :granularity nil :parent #172) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 4083 :end 5167 :pre-blank 1 :contents-begin 4115 :contents-end 5166 :robust-begin 4117 :robust-end 5164 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4083 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #183))) :mode section :granularity nil :parent #180) (section (:begin 4115 :end 5167 :contents-begin 4115 :contents-end 5166 :robust-begin 4115 :robust-end 5164 :post-blank 1 :post-affiliated 4115 :mode section :granularity nil :parent #183) (paragraph (:begin 4115 :end 4250 :contents-begin 4115 :contents-end 4249 :post-blank 1 :post-affiliated 4115 :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 4250 :end 4277 :contents-begin 4250 :contents-end 4276 :post-blank 1 :post-affiliated 4250 :mode nil :granularity nil :parent #186) #("As root configure and run\n" 0 26 (:parent #190))) (src-block (:language "bash" :switches nil :parameters nil :begin 4277 :end 4535 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mysql && addgroup mysql\nmysqld --datadir=/var/mysql --initialize-insecure\nmkdir -p /var/run/mysqld\nchown mysql.mysql ~/mysql /var/run/mysqld\nmysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 4277 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4535 :end 4583 :contents-begin 4535 :contents-end 4582 :post-blank 1 :post-affiliated 4535 :mode nil :granularity nil :parent #186) #("If you want to run as root you may have to set\n" 0 47 (:parent #192))) (fixed-width (:begin 4583 :end 4621 :value "/etc/my.cnf\n[mysqld]\nuser=root" :post-blank 2 :post-affiliated 4583 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4621 :end 4690 :contents-begin 4621 :contents-end 4689 :post-blank 1 :post-affiliated 4621 :mode nil :granularity nil :parent #186) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #194))) (fixed-width (:begin 4690 :end 4799 :value "mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log" :post-blank 2 :post-affiliated 4690 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4799 :end 4875 :contents-begin 4799 :contents-end 4874 :post-blank 1 :post-affiliated 4799 :mode nil :granularity nil :parent #186) #("Other tips are that Guix installs mysqld in your profile, so this may work\n" 0 75 (:parent #196))) (fixed-width (:begin 4875 :end 4979 :value "/home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql" :post-blank 2 :post-affiliated 4875 :mode nil :granularity nil :parent #186)) (paragraph (:begin 4979 :end 5006 :contents-begin 4979 :contents-end 5005 :post-blank 1 :post-affiliated 4979 :mode nil :granularity nil :parent #186) #("When you get errors like:\n" 0 26 (:parent #198))) (fixed-width (:begin 5006 :end 5118 :value "qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 5006 :mode nil :granularity nil :parent #186)) (paragraph (:begin 5118 :end 5139 :contents-begin 5118 :contents-end 5138 :post-blank 1 :post-affiliated 5118 :mode nil :granularity nil :parent #186) #("you may need to set\n" 0 20 (:parent #200))) (fixed-width (:begin 5139 :end 5166 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 5139 :mode nil :granularity nil :parent #186)))) (headline (:raw-value "Load the small database in MySQL" :begin 5167 :end 6699 :pre-blank 1 :contents-begin 5204 :contents-end 6698 :robust-begin 5206 :robust-end 6696 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5167 :title (#("Load the small database in MySQL" 0 32 (:parent #184))) :mode nil :granularity nil :parent #180) (section (:begin 5204 :end 6699 :contents-begin 5204 :contents-end 6698 :robust-begin 5204 :robust-end 6696 :post-blank 1 :post-affiliated 5204 :mode section :granularity nil :parent #184) (paragraph (:begin 5204 :end 5511 :contents-begin 5204 :contents-end 5510 :post-blank 1 :post-affiliated 5204 :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 5367 :end 5374 :use-brackets-p nil :contents-begin 5368 :contents-end 5374 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #194))) (subscript (:begin 5374 :end 5376 :use-brackets-p nil :contents-begin 5375 :contents-end 5376 :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 5452 :end 5459 :use-brackets-p nil :contents-begin 5453 :contents-end 5459 :post-blank 0 :parent #190) #("webqtl" 0 6 (:parent #197))) (subscript (:begin 5459 :end 5465 :use-brackets-p nil :contents-begin 5460 :contents-end 5465 :post-blank 0 :parent #190) #("plant" 0 5 (:parent #198))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #190))) (paragraph (:begin 5511 :end 5539 :contents-begin 5511 :contents-end 5538 :post-blank 1 :post-affiliated 5511 :mode nil :granularity nil :parent #187) #("Download one database from\n" 0 27 (:parent #191))) (paragraph (:begin 5539 :end 5587 :contents-begin 5539 :contents-end 5586 :post-blank 1 :post-affiliated 5539 :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 5539 :end 5585 :contents-begin nil :contents-end nil :post-blank 0 :parent #192)) #("\n" 0 1 (:parent #192))) (paragraph (:begin 5587 :end 5646 :contents-begin 5587 :contents-end 5645 :post-blank 1 :post-affiliated 5587 :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 5587 :end 5644 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 5646 :end 5665 :contents-begin 5646 :contents-end 5664 :post-blank 1 :post-affiliated 5646 :mode nil :granularity nil :parent #187) #("Check the md5sum.\n" 0 18 (:parent #194))) (paragraph (:begin 5665 :end 5736 :contents-begin 5665 :contents-end 5735 :post-blank 1 :post-affiliated 5665 :mode nil :granularity nil :parent #187) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #195))) (fixed-width (:begin 5736 :end 5837 :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 5736 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5837 :end 5884 :contents-begin 5837 :contents-end 5883 :post-blank 1 :post-affiliated 5837 :mode nil :granularity nil :parent #187) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #197))) (fixed-width (:begin 5884 :end 5901 :value "myslq -u root" :post-blank 2 :post-affiliated 5884 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5901 :end 5906 :contents-begin 5901 :contents-end 5905 :post-blank 1 :post-affiliated 5901 :mode nil :granularity nil :parent #187) #("and\n" 0 4 (:parent #199))) (fixed-width (:begin 5906 :end 6132 :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 5906 :mode nil :granularity nil :parent #187)) (paragraph (:begin 6132 :end 6197 :contents-begin 6132 :contents-end 6196 :post-blank 1 :post-affiliated 6132 :mode nil :granularity nil :parent #187) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #201))) (fixed-width (:begin 6197 :end 6296 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 6197 :mode nil :granularity nil :parent #187)) (paragraph (:begin 6296 :end 6403 :contents-begin 6296 :contents-end 6402 :post-blank 1 :post-affiliated 6296 :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 6403 :end 6566 :contents-begin 6403 :contents-end 6565 :post-blank 1 :post-affiliated 6403 :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 6566 :end 6698 :contents-begin 6566 :contents-end 6698 :post-blank 0 :post-affiliated 6566 :mode nil :granularity nil :parent #187) #("Note for the plant database you can rename it to db" 0 51 (:parent #205)) (subscript (:begin 6617 :end 6624 :use-brackets-p nil :contents-begin 6618 :contents-end 6624 :post-blank 0 :parent #205) #("webqtl" 0 6 (:parent #209))) (subscript (:begin 6624 :end 6626 :use-brackets-p nil :contents-begin 6625 :contents-end 6626 :post-blank 0 :parent #205) #("s" 0 1 (:parent #210))) #(", or\nchange the settings in etc/default" 0 39 (:parent #205)) (subscript (:begin 6665 :end 6678 :use-brackets-p nil :contents-begin 6666 :contents-end 6677 :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 6699 :end 6863 :pre-blank 1 :contents-begin 6723 :contents-end 6862 :robust-begin 6725 :robust-end 6860 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6699 :title (#("GN2 Dependency Graph" 0 20 (:parent #181))) :mode nil :granularity nil :parent #172) (section (:begin 6723 :end 6863 :contents-begin 6723 :contents-end 6862 :robust-begin 6723 :robust-end 6860 :post-blank 1 :post-affiliated 6723 :mode section :granularity nil :parent #181) (paragraph (:begin 6723 :end 6784 :contents-begin 6723 :contents-end 6783 :post-blank 1 :post-affiliated 6723 :mode planning :granularity nil :parent #184) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #187))) (paragraph (:begin 6784 :end 6862 :contents-begin 6814 :contents-end 6862 :post-blank 0 :post-affiliated 6814 :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 6814 :end 6861 :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 6863 :end 6925 :pre-blank 1 :contents-begin 6899 :contents-end 6924 :robust-begin 6901 :robust-end 6922 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6863 :title (#("Working with the GN2 source code" 0 32 (:parent #182))) :mode nil :granularity nil :parent #172) (section (:begin 6899 :end 6925 :contents-begin 6899 :contents-end 6924 :robust-begin 6899 :robust-end 6922 :post-blank 1 :post-affiliated 6899 :mode section :granularity nil :parent #182) (paragraph (:begin 6899 :end 6924 :contents-begin 6899 :contents-end 6924 :post-blank 0 :post-affiliated 6899 :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 6903 :end 6922 :contents-begin nil :contents-end nil :post-blank 0 :parent #188)) #(".\n" 0 2 (:parent #188))))) (headline (:raw-value "Running ElasticSearch" :begin 6925 :end 7675 :pre-blank 1 :contents-begin 6950 :contents-end 7674 :robust-begin 6952 :robust-end 7672 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6925 :title (#("Running ElasticSearch" 0 21 (:parent #183))) :parent #172 :cached t :granularity nil) (section (:begin 6950 :end 7134 :contents-begin 6950 :contents-end 7132 :robust-begin 6950 :robust-end 7130 :post-blank 2 :post-affiliated 6950 :mode section :granularity nil :parent #183) (paragraph (:begin 6950 :end 7132 :contents-begin 6950 :contents-end 7132 :post-blank 0 :post-affiliated 6950 :mode planning :granularity nil :parent #186) #("In order to start up elasticsearch:\nPenguin - change user to \"elasticsearch\" and use the following command: \"env JAVA" 0 117 (:parent #189)) (subscript (:begin 7067 :end 7072 :use-brackets-p nil :contents-begin 7068 :contents-end 7072 :post-blank 0 :parent #189) #("HOME" 0 4 (:parent #193))) #("=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch\"\n" 0 60 (:parent #189)))) (headline (:raw-value "SystemD" :begin 7134 :end 7675 :pre-blank 1 :contents-begin 7146 :contents-end 7674 :robust-begin 7148 :robust-end 7672 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7134 :title (#("SystemD" 0 7 (:parent #187))) :parent #183 :cached t :org-element--cache-sync-key (1 . 7134) :granularity nil) (section (:begin 7146 :end 7675 :contents-begin 7146 :contents-end 7674 :robust-begin 7146 :robust-end 7672 :post-blank 1 :post-affiliated 7146 :mode section :granularity nil :parent #187) (paragraph (:begin 7146 :end 7206 :contents-begin 7146 :contents-end 7205 :post-blank 1 :post-affiliated 7146 :mode planning :granularity nil :parent #190) #("New server - as root run \"systemctl restart elasticsearch\"\n" 0 59 (:parent #193))) (src-block (:language nil :switches nil :parameters nil :begin 7206 :end 7674 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "tux01:/etc/systemd/system# cat elasticsearch.service\n[Unit]\nDescription=Run Elasticsearch\n\n[Service]\nExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch\nEnvironment=JAVA_HOME=/opt/jdk-9.0.4\nEnvironment=\"ES_JAVA_OPTS=-Xms1g -Xmx8g\"\nEnvironment=\"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin\"\nLimitNOFILE=65536\nStandardOutput=syslog\nStandardError=syslog\nUser=elasticsearch\n\n[Install]\nWantedBy=multi-user.target\n" :post-blank 0 :post-affiliated 7206 :mode nil :granularity nil :parent #190))))) (headline (:raw-value "Read more" :begin 7675 :end 7825 :pre-blank 1 :contents-begin 7688 :contents-end 7824 :robust-begin 7690 :robust-end 7822 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7675 :title (#("Read more" 0 9 (:parent #184))) :mode nil :granularity nil :parent #172) (section (:begin 7688 :end 7825 :contents-begin 7688 :contents-end 7824 :robust-begin 7688 :robust-end 7822 :post-blank 1 :post-affiliated 7688 :mode section :granularity nil :parent #184) (paragraph (:begin 7688 :end 7824 :contents-begin 7688 :contents-end 7824 :post-blank 0 :post-affiliated 7688 :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 7743 :end 7763 :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 "Trouble shooting" :begin 7825 :end 10276 :pre-blank 1 :contents-begin 7845 :contents-end 10274 :robust-begin 7847 :robust-end 10272 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7825 :title (#("Trouble shooting" 0 16 (:parent #185))) :mode nil :granularity nil :parent #172) (headline (:raw-value "ImportError: No module named jinja2" :begin 7845 :end 8379 :pre-blank 1 :contents-begin 7885 :contents-end 8379 :robust-begin 7887 :robust-end 8377 :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 7845 :title (#("ImportError: No module named jinja2" 0 35 (:parent #188))) :mode section :granularity nil :parent #185) (section (:begin 7885 :end 8379 :contents-begin 7885 :contents-end 8379 :robust-begin 7885 :robust-end 8377 :post-blank 0 :post-affiliated 7885 :mode section :granularity nil :parent #188) (paragraph (:begin 7885 :end 8120 :contents-begin 7885 :contents-end 8119 :post-blank 1 :post-affiliated 7885 :mode planning :granularity nil :parent #191) #("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 #194)) (subscript (:begin 8052 :end 8058 :use-brackets-p nil :contents-begin 8053 :contents-end 8057 :post-blank 1 :parent #194) #("PATH" 0 4 (:parent #198))) #("and R" 0 5 (:parent #194)) (subscript (:begin 8063 :end 8068 :use-brackets-p nil :contents-begin 8064 :contents-end 8068 :post-blank 0 :parent #194) #("LIBS" 0 4 (:parent #200))) (subscript (:begin 8068 :end 8074 :use-brackets-p nil :contents-begin 8069 :contents-end 8073 :post-blank 1 :parent #194) #("SITE" 0 4 (:parent #201))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #194))) (fixed-width (:begin 8120 :end 8151 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8120 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8151 :end 8167 :contents-begin 8151 :contents-end 8166 :post-blank 1 :post-affiliated 8151 :mode nil :granularity nil :parent #191) #("On one system:\n" 0 15 (:parent #196))) (fixed-width (:begin 8167 :end 8355 :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 8167 :mode nil :granularity nil :parent #191)) (paragraph (:begin 8355 :end 8379 :contents-begin 8355 :contents-end 8379 :post-blank 0 :post-affiliated 8355 :mode nil :granularity nil :parent #191) #("and perhaps a few more.\n" 0 24 (:parent #198))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 8379 :end 8875 :pre-blank 1 :contents-begin 8488 :contents-end 8874 :robust-begin 8490 :robust-end 8872 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8379 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #189)) (subscript (:begin 8422 :end 8427 :use-brackets-p nil :contents-begin 8423 :contents-end 8427 :post-blank 0 :parent #189) #("data" 0 4 (:parent #231))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #189)) (subscript (:begin 8470 :end 8476 :use-brackets-p nil :contents-begin 8471 :contents-end 8476 :post-blank 0 :parent #189) #("files" 0 5 (:parent #233))) #("/genotype'" 0 10 (:parent #189))) :mode nil :granularity nil :parent #185) (section (:begin 8488 :end 8875 :contents-begin 8488 :contents-end 8874 :robust-begin 8488 :robust-end 8872 :post-blank 1 :post-affiliated 8488 :mode section :granularity nil :parent #189) (paragraph (:begin 8488 :end 8710 :contents-begin 8488 :contents-end 8709 :post-blank 1 :post-affiliated 8488 :mode planning :granularity nil :parent #192) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #195)) (subscript (:begin 8537 :end 8542 :use-brackets-p nil :contents-begin 8538 :contents-end 8542 :post-blank 0 :parent #195) #("data" 0 4 (:parent #199))) #(". 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 #195)) (subscript (:begin 8666 :end 8679 :use-brackets-p nil :contents-begin 8667 :contents-end 8678 :post-blank 1 :parent #195) #("settings.py" 0 11 (:parent #201))) #("(see above in\nthis document).\n" 0 30 (:parent #195))) (paragraph (:begin 8710 :end 8784 :contents-begin 8710 :contents-end 8783 :post-blank 1 :post-affiliated 8710 :mode nil :granularity nil :parent #192) #("You can use the GENENETWORK" 0 27 (:parent #196)) (subscript (:begin 8737 :end 8744 :use-brackets-p nil :contents-begin 8738 :contents-end 8743 :post-blank 1 :parent #196) #("FILES" 0 5 (:parent #200))) #("switch to set the datadir, for example\n" 0 39 (:parent #196))) (fixed-width (:begin 8784 :end 8874 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 8784 :mode nil :granularity nil :parent #192)))) (headline (:raw-value "Can't run a module" :begin 8875 :end 9109 :pre-blank 1 :contents-begin 8898 :contents-end 9109 :robust-begin 8900 :robust-end 9107 :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 8875 :title (#("Can't run a module" 0 18 (:parent #190))) :mode nil :granularity nil :parent #185) (section (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :robust-begin 8898 :robust-end 9107 :post-blank 0 :post-affiliated 8898 :mode section :granularity nil :parent #190) (paragraph (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :post-blank 0 :post-affiliated 8898 :mode planning :granularity nil :parent #193) #("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 #196))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 9109 :end 9610 :pre-blank 1 :contents-begin 9141 :contents-end 9609 :robust-begin 9143 :robust-end 9607 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9109 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #191))) :mode nil :granularity nil :parent #185) (section (:begin 9141 :end 9610 :contents-begin 9141 :contents-end 9609 :robust-begin 9141 :robust-end 9607 :post-blank 1 :post-affiliated 9141 :mode section :granularity nil :parent #191) (paragraph (:begin 9141 :end 9153 :contents-begin 9141 :contents-end 9152 :post-blank 1 :post-affiliated 9141 :mode planning :granularity nil :parent #194) #("This error\n" 0 11 (:parent #197))) (fixed-width (:begin 9153 :end 9233 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 9153 :mode nil :granularity nil :parent #194)) (paragraph (:begin 9233 :end 9364 :contents-begin 9233 :contents-end 9363 :post-blank 1 :post-affiliated 9233 :mode nil :granularity nil :parent #194) #("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 #199))) (paragraph (:begin 9364 :end 9609 :contents-begin 9364 :contents-end 9609 :post-blank 0 :post-affiliated 9364 :mode nil :granularity nil :parent #194) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #200)) (subscript (:begin 9427 :end 9432 :use-brackets-p nil :contents-begin 9428 :contents-end 9432 :post-blank 0 :parent #200) #("LIBS" 0 4 (:parent #204))) (subscript (:begin 9432 :end 9437 :use-brackets-p nil :contents-begin 9433 :contents-end 9437 :post-blank 0 :parent #200) #("SITE" 0 4 (:parent #205))) #(". 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 #200))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 9610 :end 10276 :pre-blank 1 :contents-begin 9662 :contents-end 10274 :robust-begin 9664 :robust-end 10272 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9610 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #192))) :mode nil :granularity nil :parent #185) (section (:begin 9662 :end 10276 :contents-begin 9662 :contents-end 10274 :robust-begin 9662 :robust-end 10272 :post-blank 2 :post-affiliated 9662 :mode section :granularity nil :parent #192) (paragraph (:begin 9662 :end 9683 :contents-begin 9662 :contents-end 9682 :post-blank 1 :post-affiliated 9662 :mode planning :granularity nil :parent #195) #("The following error\n" 0 20 (:parent #198))) (fixed-width (:begin 9683 :end 9878 :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 9683 :mode nil :granularity nil :parent #195)) (paragraph (:begin 9878 :end 10036 :contents-begin 9878 :contents-end 10035 :post-blank 1 :post-affiliated 9878 :mode nil :granularity nil :parent #195) #("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 #200))) (fixed-width (:begin 10036 :end 10058 :value "mysql -h localhost" :post-blank 2 :post-affiliated 10036 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10058 :end 10115 :contents-begin 10058 :contents-end 10114 :post-blank 1 :post-affiliated 10058 :mode nil :granularity nil :parent #195) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #202))) (fixed-width (:begin 10115 :end 10137 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 10115 :mode nil :granularity nil :parent #195)) (paragraph (:begin 10137 :end 10208 :contents-begin 10137 :contents-end 10207 :post-blank 1 :post-affiliated 10137 :mode nil :granularity nil :parent #195) #("if that works run genenetwork after setting SQL" 0 47 (:parent #204)) (subscript (:begin 10184 :end 10189 :use-brackets-p nil :contents-begin 10185 :contents-end 10188 :post-blank 1 :parent #204) #("URI" 0 3 (:parent #208))) #("to something like\n" 0 18 (:parent #204))) (fixed-width (:begin 10208 :end 10274 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 10208 :mode nil :granularity nil :parent #195))))) (headline (:raw-value "IRC session" :begin 10276 :end 14428 :pre-blank 1 :contents-begin 10291 :contents-end 14428 :robust-begin 10293 :robust-end 14426 :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 10276 :title (#("IRC session" 0 11 (:parent #186))) :mode nil :granularity nil :parent #172) (section (:begin 10291 :end 14428 :contents-begin 10291 :contents-end 14428 :robust-begin 10291 :robust-end 14426 :post-blank 0 :post-affiliated 10291 :mode section :granularity nil :parent #186) (paragraph (:begin 10291 :end 10400 :contents-begin 10291 :contents-end 10399 :post-blank 1 :post-affiliated 10291 :mode planning :granularity nil :parent #189) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #192))) (paragraph (:begin 10400 :end 10961 :contents-begin 10400 :contents-end 10960 :post-blank 1 :post-affiliated 10400 :mode nil :granularity nil :parent #189) #("#+begin" 0 7 (:parent #193)) (subscript (:begin 10407 :end 10411 :use-brackets-p nil :contents-begin 10408 :contents-end 10411 :post-blank 0 :parent #193) #("src" 0 3 (:parent #197))) #("\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 #193))) (paragraph (:begin 10961 :end 11051 :contents-begin 10961 :contents-end 11050 :post-blank 1 :post-affiliated 10961 :mode nil :granularity nil :parent #189) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #194))) (paragraph (:begin 11051 :end 11196 :contents-begin 11051 :contents-end 11195 :post-blank 1 :post-affiliated 11051 :mode nil :granularity nil :parent #189) #(" yes\n env GUIX" 0 30 (:parent #195)) (subscript (:begin 11081 :end 11089 :use-brackets-p nil :contents-begin 11082 :contents-end 11089 :post-blank 0 :parent #195) #("PACKAGE" 0 7 (:parent #199))) (subscript (:begin 11089 :end 11094 :use-brackets-p nil :contents-begin 11090 :contents-end 11094 :post-blank 0 :parent #195) #("PATH" 0 4 (:parent #200))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #195))) (paragraph (:begin 11196 :end 11492 :contents-begin 11196 :contents-end 11491 :post-blank 1 :post-affiliated 11196 :mode nil :granularity nil :parent #189) #("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 #196))) (paragraph (:begin 11492 :end 12685 :contents-begin 11492 :contents-end 12684 :post-blank 1 :post-affiliated 11492 :mode nil :granularity nil :parent #189) #(" 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 #197)) (subscript (:begin 12245 :end 12253 :use-brackets-p nil :contents-begin 12246 :contents-end 12253 :post-blank 0 :parent #197) #("PACKAGE" 0 7 (:parent #201))) (subscript (:begin 12253 :end 12258 :use-brackets-p nil :contents-begin 12254 :contents-end 12258 :post-blank 0 :parent #197) #("PATH" 0 4 (:parent #202))) #("=../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 #197))) (paragraph (:begin 12685 :end 12889 :contents-begin 12685 :contents-end 12888 :post-blank 1 :post-affiliated 12685 :mode nil :granularity nil :parent #189) #("/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 #198))) (paragraph (:begin 12889 :end 14428 :contents-begin 12889 :contents-end 14428 :post-blank 0 :post-affiliated 12889 :mode nil :granularity nil :parent #189) #(" which should have the same HASH values " 0 48 (:parent #199)) (italic (:begin 12937 :end 13846 :post-blank 0 :contents-begin 12938 :contents-end 13845 :parent #199) #("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 #203))) #(".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" 0 582 (:parent #199))))))) #102)) #78)) #46 (item (:bullet "- " :begin 156 :end 268 :contents-begin 159 :contents-end 268 :checkbox nil :counter nil :structure ((121 1 "- " nil nil 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Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1932 :end 2008 :contents-begin 1986 :contents-end 2005 :post-blank 1 :parent #185) #("Guix bioinformatics" 0 19 (:parent #189))) #("and " 0 4 (:parent #185)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2012 :end 2061 :contents-begin 2051 :contents-end 2059 :post-blank 0 :parent #185) #("GNU Guix" 0 8 (:parent #191))) #(".\n" 0 2 (:parent #185))) (paragraph (:begin 2064 :end 2199 :contents-begin 2064 :contents-end 2199 :post-blank 0 :post-affiliated 2064 :mode nil :granularity nil :parent #181) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #186)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2150 :end 2197 :contents-begin 2175 :contents-end 2195 :post-blank 0 :parent #186) #("GN2 Dependency Graph" 0 20 (:parent #190))) #(".\n" 0 2 (:parent #186))))) (headline (:raw-value "Install" :begin 2200 :end 3583 :pre-blank 1 :contents-begin 2211 :contents-end 3582 :robust-begin 2213 :robust-end 3580 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2200 :title (#("Install" 0 7 (:parent #179))) :mode nil :granularity nil :parent #173) (section (:begin 2211 :end 2575 :contents-begin 2211 :contents-end 2574 :robust-begin 2211 :robust-end 2572 :post-blank 1 :post-affiliated 2211 :mode section :granularity nil :parent #179) (paragraph (:begin 2211 :end 2574 :contents-begin 2211 :contents-end 2574 :post-blank 0 :post-affiliated 2211 :mode planning :granularity nil :parent #182) #("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 #185)))) (headline (:raw-value "Tarball" :begin 2575 :end 3228 :pre-blank 1 :contents-begin 2587 :contents-end 3227 :robust-begin 2589 :robust-end 3225 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2575 :title (#("Tarball" 0 7 (:parent #183))) :mode nil :granularity nil :parent #179) (section (:begin 2587 :end 3228 :contents-begin 2587 :contents-end 3227 :robust-begin 2587 :robust-end 3225 :post-blank 1 :post-affiliated 2587 :mode section :granularity nil :parent #183) (paragraph (:begin 2587 :end 2734 :contents-begin 2587 :contents-end 2733 :post-blank 1 :post-affiliated 2587 :mode planning :granularity nil :parent #186) #("Download the ~800Mb tarball from\n" 0 33 (:parent #189)) (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 2620 :end 2677 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(". Validate the checksum and\nunpack to root, for example\n" 0 56 (:parent #189))) (fixed-width (:begin 2734 :end 2836 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2734 :mode nil :granularity nil :parent #186)) (paragraph (:begin 2836 :end 2884 :contents-begin 2836 :contents-end 2883 :post-blank 1 :post-affiliated 2836 :mode nil :granularity nil :parent #186) #("Now you shoud be able to start the server with\n" 0 47 (:parent #191))) (fixed-width (:begin 2884 :end 2922 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2884 :mode nil :granularity nil :parent #186)) (paragraph (:begin 2922 :end 3049 :contents-begin 2922 :contents-end 3048 :post-blank 1 :post-affiliated 2922 :mode nil :granularity nil :parent #186) #("When the server stops with a MySQL error " 0 41 (:parent #193)) (link (:type "custom-id" :path "run-mysql-server" :format bracket :raw-link "#run-mysql-server" :application nil :search-option nil :begin 2963 :end 3002 :contents-begin 2984 :contents-end 3000 :post-blank 0 :parent #193) #("Run MySQL server" 0 16 (:parent #197))) #("\nand set SQL" 0 12 (:parent #193)) (subscript (:begin 3014 :end 3019 :use-brackets-p nil :contents-begin 3015 :contents-end 3018 :post-blank 1 :parent #193) #("URI" 0 3 (:parent #199))) #("to point at it. For example:\n" 0 29 (:parent #193))) (fixed-width (:begin 3049 :end 3116 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 3049 :mode nil :granularity nil :parent #186)) (paragraph (:begin 3116 :end 3227 :contents-begin 3116 :contents-end 3227 :post-blank 0 :post-affiliated 3116 :mode nil :granularity nil :parent #186) #("See also " 0 9 (:parent #195)) (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 3125 :end 3225 :contents-begin 3176 :contents-end 3223 :post-blank 0 :parent #195) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #199))) #(".\n" 0 2 (:parent #195))))) (headline (:raw-value "Docker" :begin 3228 :end 3437 :pre-blank 1 :contents-begin 3239 :contents-end 3436 :robust-begin 3241 :robust-end 3434 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3228 :title (#("Docker" 0 6 (:parent #184))) :mode nil :granularity nil :parent #179) (section (:begin 3239 :end 3437 :contents-begin 3239 :contents-end 3436 :robust-begin 3239 :robust-end 3434 :post-blank 1 :post-affiliated 3239 :mode section :granularity nil :parent #184) (paragraph (:begin 3239 :end 3436 :contents-begin 3239 :contents-end 3436 :post-blank 0 :post-affiliated 3239 :mode planning :granularity nil :parent #187) #("Docker images are also available through\n" 0 41 (:parent #190)) (link (:type "http" :path "//files.genenetwork.org/software/" :format bracket :raw-link "http://files.genenetwork.org/software/" :application nil :search-option nil :begin 3280 :end 3322 :contents-begin nil :contents-end nil :post-blank 0 :parent #190)) #(". Validate the checksum and run\nwith " 0 37 (:parent #190)) (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 3359 :end 3434 :contents-begin 3421 :contents-end 3432 :post-blank 0 :parent #190) #("Docker load" 0 11 (:parent #196))) #(".\n" 0 2 (:parent #190))))) (headline (:raw-value "With source" :begin 3437 :end 3583 :pre-blank 1 :contents-begin 3453 :contents-end 3582 :robust-begin 3455 :robust-end 3580 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3437 :title (#("With source" 0 11 (:parent #185))) :mode nil :granularity nil :parent #179) (section (:begin 3453 :end 3583 :contents-begin 3453 :contents-end 3582 :robust-begin 3453 :robust-end 3580 :post-blank 1 :post-affiliated 3453 :mode section :granularity nil :parent #185) (paragraph (:begin 3453 :end 3582 :contents-begin 3453 :contents-end 3582 :post-blank 0 :post-affiliated 3453 :mode planning :granularity nil :parent #188) #("For more elaborate installation instructions on deploying GeneNetwork from\nsource see " 0 86 (:parent #191)) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 3539 :end 3580 :contents-begin 3561 :contents-end 3578 :post-blank 0 :parent #191) #("Source deployment" 0 17 (:parent #195))) #(".\n" 0 2 (:parent #191)))))) (headline (:raw-value "Running GN2" :begin 3583 :end 4064 :pre-blank 1 :contents-begin 3598 :contents-end 4063 :robust-begin 3600 :robust-end 4061 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3583 :title (#("Running GN2" 0 11 (:parent #180))) :mode nil :granularity nil :parent #173) (section (:begin 3598 :end 4064 :contents-begin 3598 :contents-end 4063 :robust-begin 3598 :robust-end 4061 :post-blank 1 :post-affiliated 3598 :mode section :granularity nil :parent #180) (paragraph (:begin 3598 :end 3793 :contents-begin 3598 :contents-end 3792 :post-blank 1 :post-affiliated 3598 :mode planning :granularity nil :parent #183) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #186)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 3651 :end 3702 :contents-begin 3681 :contents-end 3700 :post-blank 0 :parent #186) #("default" 0 7 (:parent #190)) (subscript (:begin 3688 :end 3700 :use-brackets-p nil :contents-begin 3689 :contents-end 3700 :post-blank 0 :parent #190) #("settings.py" 0 11 (:parent #194)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #186))) (fixed-width (:begin 3793 :end 3823 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3793 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3823 :end 3901 :contents-begin 3823 :contents-end 3900 :post-blank 1 :post-affiliated 3823 :mode nil :granularity nil :parent #183) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #188))) (fixed-width (:begin 3901 :end 3984 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3901 :mode nil :granularity nil :parent #183)) (paragraph (:begin 3984 :end 4063 :contents-begin 3984 :contents-end 4063 :post-blank 0 :post-affiliated 3984 :mode nil :granularity nil :parent #183) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #190))))) (headline (:raw-value "Run MySQL server" :begin 4064 :end 6699 :pre-blank 0 :contents-begin 4083 :contents-end 6698 :robust-begin 4085 :robust-end 6696 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4064 :title (#("Run MySQL server" 0 16 (:parent #181))) :mode nil :granularity nil :parent #173) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 4083 :end 5167 :pre-blank 1 :contents-begin 4115 :contents-end 5166 :robust-begin 4117 :robust-end 5164 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4083 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #184))) :mode section :granularity nil :parent #181) (section (:begin 4115 :end 5167 :contents-begin 4115 :contents-end 5166 :robust-begin 4115 :robust-end 5164 :post-blank 1 :post-affiliated 4115 :mode section :granularity nil :parent #184) (paragraph (:begin 4115 :end 4250 :contents-begin 4115 :contents-end 4249 :post-blank 1 :post-affiliated 4115 :mode planning :granularity nil :parent #187) #("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 #190))) (paragraph (:begin 4250 :end 4277 :contents-begin 4250 :contents-end 4276 :post-blank 1 :post-affiliated 4250 :mode nil :granularity nil :parent #187) #("As root configure and run\n" 0 26 (:parent #191))) (src-block (:language "bash" :switches nil :parameters nil :begin 4277 :end 4535 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mysql && addgroup mysql\nmysqld --datadir=/var/mysql --initialize-insecure\nmkdir -p /var/run/mysqld\nchown mysql.mysql ~/mysql /var/run/mysqld\nmysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 4277 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4535 :end 4583 :contents-begin 4535 :contents-end 4582 :post-blank 1 :post-affiliated 4535 :mode nil :granularity nil :parent #187) #("If you want to run as root you may have to set\n" 0 47 (:parent #193))) (fixed-width (:begin 4583 :end 4621 :value "/etc/my.cnf\n[mysqld]\nuser=root" :post-blank 2 :post-affiliated 4583 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4621 :end 4690 :contents-begin 4621 :contents-end 4689 :post-blank 1 :post-affiliated 4621 :mode nil :granularity nil :parent #187) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #195))) (fixed-width (:begin 4690 :end 4799 :value "mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log" :post-blank 2 :post-affiliated 4690 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4799 :end 4875 :contents-begin 4799 :contents-end 4874 :post-blank 1 :post-affiliated 4799 :mode nil :granularity nil :parent #187) #("Other tips are that Guix installs mysqld in your profile, so this may work\n" 0 75 (:parent #197))) (fixed-width (:begin 4875 :end 4979 :value "/home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql" :post-blank 2 :post-affiliated 4875 :mode nil :granularity nil :parent #187)) (paragraph (:begin 4979 :end 5006 :contents-begin 4979 :contents-end 5005 :post-blank 1 :post-affiliated 4979 :mode nil :granularity nil :parent #187) #("When you get errors like:\n" 0 26 (:parent #199))) (fixed-width (:begin 5006 :end 5118 :value "qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 5006 :mode nil :granularity nil :parent #187)) (paragraph (:begin 5118 :end 5139 :contents-begin 5118 :contents-end 5138 :post-blank 1 :post-affiliated 5118 :mode nil :granularity nil :parent #187) #("you may need to set\n" 0 20 (:parent #201))) (fixed-width (:begin 5139 :end 5166 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 5139 :mode nil :granularity nil :parent #187)))) (headline (:raw-value "Load the small database in MySQL" :begin 5167 :end 6699 :pre-blank 1 :contents-begin 5204 :contents-end 6698 :robust-begin 5206 :robust-end 6696 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5167 :title (#("Load the small database in MySQL" 0 32 (:parent #185))) :mode nil :granularity nil :parent #181) (section (:begin 5204 :end 6699 :contents-begin 5204 :contents-end 6698 :robust-begin 5204 :robust-end 6696 :post-blank 1 :post-affiliated 5204 :mode section :granularity nil :parent #185) (paragraph (:begin 5204 :end 5511 :contents-begin 5204 :contents-end 5510 :post-blank 1 :post-affiliated 5204 :mode planning :granularity nil :parent #188) #("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 #191)) (subscript (:begin 5367 :end 5374 :use-brackets-p nil :contents-begin 5368 :contents-end 5374 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #195))) (subscript (:begin 5374 :end 5376 :use-brackets-p nil :contents-begin 5375 :contents-end 5376 :post-blank 0 :parent #191) #("s" 0 1 (:parent #196))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #191)) (subscript (:begin 5452 :end 5459 :use-brackets-p nil :contents-begin 5453 :contents-end 5459 :post-blank 0 :parent #191) #("webqtl" 0 6 (:parent #198))) (subscript (:begin 5459 :end 5465 :use-brackets-p nil :contents-begin 5460 :contents-end 5465 :post-blank 0 :parent #191) #("plant" 0 5 (:parent #199))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #191))) (paragraph (:begin 5511 :end 5539 :contents-begin 5511 :contents-end 5538 :post-blank 1 :post-affiliated 5511 :mode nil :granularity nil :parent #188) #("Download one database from\n" 0 27 (:parent #192))) (paragraph (:begin 5539 :end 5587 :contents-begin 5539 :contents-end 5586 :post-blank 1 :post-affiliated 5539 :mode nil :granularity nil :parent #188) (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 5539 :end 5585 :contents-begin nil :contents-end nil :post-blank 0 :parent #193)) #("\n" 0 1 (:parent #193))) (paragraph (:begin 5587 :end 5646 :contents-begin 5587 :contents-end 5645 :post-blank 1 :post-affiliated 5587 :mode nil :granularity nil :parent #188) (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 5587 :end 5644 :contents-begin nil :contents-end nil :post-blank 0 :parent #194)) #("\n" 0 1 (:parent #194))) (paragraph (:begin 5646 :end 5665 :contents-begin 5646 :contents-end 5664 :post-blank 1 :post-affiliated 5646 :mode nil :granularity nil :parent #188) #("Check the md5sum.\n" 0 18 (:parent #195))) (paragraph (:begin 5665 :end 5736 :contents-begin 5665 :contents-end 5735 :post-blank 1 :post-affiliated 5665 :mode nil :granularity nil :parent #188) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #196))) (fixed-width (:begin 5736 :end 5837 :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 5736 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5837 :end 5884 :contents-begin 5837 :contents-end 5883 :post-blank 1 :post-affiliated 5837 :mode nil :granularity nil :parent #188) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #198))) (fixed-width (:begin 5884 :end 5901 :value "myslq -u root" :post-blank 2 :post-affiliated 5884 :mode nil :granularity nil :parent #188)) (paragraph (:begin 5901 :end 5906 :contents-begin 5901 :contents-end 5905 :post-blank 1 :post-affiliated 5901 :mode nil :granularity nil :parent #188) #("and\n" 0 4 (:parent #200))) (fixed-width (:begin 5906 :end 6132 :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 5906 :mode nil :granularity nil :parent #188)) (paragraph (:begin 6132 :end 6197 :contents-begin 6132 :contents-end 6196 :post-blank 1 :post-affiliated 6132 :mode nil :granularity nil :parent #188) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #202))) (fixed-width (:begin 6197 :end 6296 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 6197 :mode nil :granularity nil :parent #188)) (paragraph (:begin 6296 :end 6403 :contents-begin 6296 :contents-end 6402 :post-blank 1 :post-affiliated 6296 :mode nil :granularity nil :parent #188) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #204))) (paragraph (:begin 6403 :end 6566 :contents-begin 6403 :contents-end 6565 :post-blank 1 :post-affiliated 6403 :mode nil :granularity nil :parent #188) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #205))) (paragraph (:begin 6566 :end 6698 :contents-begin 6566 :contents-end 6698 :post-blank 0 :post-affiliated 6566 :mode nil :granularity nil :parent #188) #("Note for the plant database you can rename it to db" 0 51 (:parent #206)) (subscript (:begin 6617 :end 6624 :use-brackets-p nil :contents-begin 6618 :contents-end 6624 :post-blank 0 :parent #206) #("webqtl" 0 6 (:parent #210))) (subscript (:begin 6624 :end 6626 :use-brackets-p nil :contents-begin 6625 :contents-end 6626 :post-blank 0 :parent #206) #("s" 0 1 (:parent #211))) #(", or\nchange the settings in etc/default" 0 39 (:parent #206)) (subscript (:begin 6665 :end 6678 :use-brackets-p nil :contents-begin 6666 :contents-end 6677 :post-blank 1 :parent #206) #("settings.py" 0 11 (:parent #213))) #("to match your path.\n" 0 20 (:parent #206)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 6699 :end 6863 :pre-blank 1 :contents-begin 6723 :contents-end 6862 :robust-begin 6725 :robust-end 6860 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6699 :title (#("GN2 Dependency Graph" 0 20 (:parent #182))) :mode nil :granularity nil :parent #173) (section (:begin 6723 :end 6863 :contents-begin 6723 :contents-end 6862 :robust-begin 6723 :robust-end 6860 :post-blank 1 :post-affiliated 6723 :mode section :granularity nil :parent #182) (paragraph (:begin 6723 :end 6784 :contents-begin 6723 :contents-end 6783 :post-blank 1 :post-affiliated 6723 :mode planning :granularity nil :parent #185) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #188))) (paragraph (:begin 6784 :end 6862 :contents-begin 6814 :contents-end 6862 :post-blank 0 :post-affiliated 6814 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #185) (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 6814 :end 6861 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #("\n" 0 1 (:parent #189))))) (headline (:raw-value "Working with the GN2 source code" :begin 6863 :end 6925 :pre-blank 1 :contents-begin 6899 :contents-end 6924 :robust-begin 6901 :robust-end 6922 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6863 :title (#("Working with the GN2 source code" 0 32 (:parent #183))) :mode nil :granularity nil :parent #173) (section (:begin 6899 :end 6925 :contents-begin 6899 :contents-end 6924 :robust-begin 6899 :robust-end 6922 :post-blank 1 :post-affiliated 6899 :mode section :granularity nil :parent #183) (paragraph (:begin 6899 :end 6924 :contents-begin 6899 :contents-end 6924 :post-blank 0 :post-affiliated 6899 :mode planning :granularity nil :parent #186) #("See " 0 4 (:parent #189)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6903 :end 6922 :contents-begin nil :contents-end nil :post-blank 0 :parent #189)) #(".\n" 0 2 (:parent #189))))) (headline (:raw-value "Running ElasticSearch" :begin 6925 :end 7675 :pre-blank 1 :contents-begin 6950 :contents-end 7674 :robust-begin 6952 :robust-end 7672 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6925 :title (#("Running ElasticSearch" 0 21 (:parent #184))) :parent #173 :cached t :granularity nil) (section (:begin 6950 :end 7134 :contents-begin 6950 :contents-end 7132 :robust-begin 6950 :robust-end 7130 :post-blank 2 :post-affiliated 6950 :mode section :granularity nil :parent #184) (paragraph (:begin 6950 :end 7132 :contents-begin 6950 :contents-end 7132 :post-blank 0 :post-affiliated 6950 :mode planning :granularity nil :parent #187) #("In order to start up elasticsearch:\nPenguin - change user to \"elasticsearch\" and use the following command: \"env JAVA" 0 117 (:parent #190)) (subscript (:begin 7067 :end 7072 :use-brackets-p nil :contents-begin 7068 :contents-end 7072 :post-blank 0 :parent #190) #("HOME" 0 4 (:parent #194))) #("=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch\"\n" 0 60 (:parent #190)))) (headline (:raw-value "SystemD" :begin 7134 :end 7675 :pre-blank 1 :contents-begin 7146 :contents-end 7674 :robust-begin 7148 :robust-end 7672 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7134 :title (#("SystemD" 0 7 (:parent #188))) :parent #184 :cached t :org-element--cache-sync-key (1 . 7134) :granularity nil) (section (:begin 7146 :end 7675 :contents-begin 7146 :contents-end 7674 :robust-begin 7146 :robust-end 7672 :post-blank 1 :post-affiliated 7146 :mode section :granularity nil :parent #188) (paragraph (:begin 7146 :end 7206 :contents-begin 7146 :contents-end 7205 :post-blank 1 :post-affiliated 7146 :mode planning :granularity nil :parent #191) #("New server - as root run \"systemctl restart elasticsearch\"\n" 0 59 (:parent #194))) (src-block (:language nil :switches nil :parameters nil :begin 7206 :end 7674 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "tux01:/etc/systemd/system# cat elasticsearch.service\n[Unit]\nDescription=Run Elasticsearch\n\n[Service]\nExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch\nEnvironment=JAVA_HOME=/opt/jdk-9.0.4\nEnvironment=\"ES_JAVA_OPTS=-Xms1g -Xmx8g\"\nEnvironment=\"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin\"\nLimitNOFILE=65536\nStandardOutput=syslog\nStandardError=syslog\nUser=elasticsearch\n\n[Install]\nWantedBy=multi-user.target\n" :post-blank 0 :post-affiliated 7206 :mode nil :granularity nil :parent #191))))) (headline (:raw-value "Read more" :begin 7675 :end 7825 :pre-blank 1 :contents-begin 7688 :contents-end 7824 :robust-begin 7690 :robust-end 7822 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7675 :title (#("Read more" 0 9 (:parent #185))) :mode nil :granularity nil :parent #173) (section (:begin 7688 :end 7825 :contents-begin 7688 :contents-end 7824 :robust-begin 7688 :robust-end 7822 :post-blank 1 :post-affiliated 7688 :mode section :granularity nil :parent #185) (paragraph (:begin 7688 :end 7824 :contents-begin 7688 :contents-end 7824 :post-blank 0 :post-affiliated 7688 :mode planning :granularity nil :parent #188) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #191)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 7743 :end 7763 :contents-begin nil :contents-end nil :post-blank 0 :parent #191)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #191))))) (headline (:raw-value "Trouble shooting" :begin 7825 :end 10276 :pre-blank 1 :contents-begin 7845 :contents-end 10274 :robust-begin 7847 :robust-end 10272 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7825 :title (#("Trouble shooting" 0 16 (:parent #186))) :mode nil :granularity nil :parent #173) (headline (:raw-value "ImportError: No module named jinja2" :begin 7845 :end 8379 :pre-blank 1 :contents-begin 7885 :contents-end 8379 :robust-begin 7887 :robust-end 8377 :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 7845 :title (#("ImportError: No module named jinja2" 0 35 (:parent #189))) :mode section :granularity nil :parent #186) (section (:begin 7885 :end 8379 :contents-begin 7885 :contents-end 8379 :robust-begin 7885 :robust-end 8377 :post-blank 0 :post-affiliated 7885 :mode section :granularity nil :parent #189) (paragraph (:begin 7885 :end 8120 :contents-begin 7885 :contents-end 8119 :post-blank 1 :post-affiliated 7885 :mode planning :granularity nil :parent #192) #("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 #195)) (subscript (:begin 8052 :end 8058 :use-brackets-p nil :contents-begin 8053 :contents-end 8057 :post-blank 1 :parent #195) #("PATH" 0 4 (:parent #199))) #("and R" 0 5 (:parent #195)) (subscript (:begin 8063 :end 8068 :use-brackets-p nil :contents-begin 8064 :contents-end 8068 :post-blank 0 :parent #195) #("LIBS" 0 4 (:parent #201))) (subscript (:begin 8068 :end 8074 :use-brackets-p nil :contents-begin 8069 :contents-end 8073 :post-blank 1 :parent #195) #("SITE" 0 4 (:parent #202))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #195))) (fixed-width (:begin 8120 :end 8151 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8120 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8151 :end 8167 :contents-begin 8151 :contents-end 8166 :post-blank 1 :post-affiliated 8151 :mode nil :granularity nil :parent #192) #("On one system:\n" 0 15 (:parent #197))) (fixed-width (:begin 8167 :end 8355 :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 8167 :mode nil :granularity nil :parent #192)) (paragraph (:begin 8355 :end 8379 :contents-begin 8355 :contents-end 8379 :post-blank 0 :post-affiliated 8355 :mode nil :granularity nil :parent #192) #("and perhaps a few more.\n" 0 24 (:parent #199))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 8379 :end 8875 :pre-blank 1 :contents-begin 8488 :contents-end 8874 :robust-begin 8490 :robust-end 8872 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8379 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #190)) (subscript (:begin 8422 :end 8427 :use-brackets-p nil :contents-begin 8423 :contents-end 8427 :post-blank 0 :parent #190) #("data" 0 4 (:parent #232))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #190)) (subscript (:begin 8470 :end 8476 :use-brackets-p nil :contents-begin 8471 :contents-end 8476 :post-blank 0 :parent #190) #("files" 0 5 (:parent #234))) #("/genotype'" 0 10 (:parent #190))) :mode nil :granularity nil :parent #186) (section (:begin 8488 :end 8875 :contents-begin 8488 :contents-end 8874 :robust-begin 8488 :robust-end 8872 :post-blank 1 :post-affiliated 8488 :mode section :granularity nil :parent #190) (paragraph (:begin 8488 :end 8710 :contents-begin 8488 :contents-end 8709 :post-blank 1 :post-affiliated 8488 :mode planning :granularity nil :parent #193) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #196)) (subscript (:begin 8537 :end 8542 :use-brackets-p nil :contents-begin 8538 :contents-end 8542 :post-blank 0 :parent #196) #("data" 0 4 (:parent #200))) #(". 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 #196)) (subscript (:begin 8666 :end 8679 :use-brackets-p nil :contents-begin 8667 :contents-end 8678 :post-blank 1 :parent #196) #("settings.py" 0 11 (:parent #202))) #("(see above in\nthis document).\n" 0 30 (:parent #196))) (paragraph (:begin 8710 :end 8784 :contents-begin 8710 :contents-end 8783 :post-blank 1 :post-affiliated 8710 :mode nil :granularity nil :parent #193) #("You can use the GENENETWORK" 0 27 (:parent #197)) (subscript (:begin 8737 :end 8744 :use-brackets-p nil :contents-begin 8738 :contents-end 8743 :post-blank 1 :parent #197) #("FILES" 0 5 (:parent #201))) #("switch to set the datadir, for example\n" 0 39 (:parent #197))) (fixed-width (:begin 8784 :end 8874 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 8784 :mode nil :granularity nil :parent #193)))) (headline (:raw-value "Can't run a module" :begin 8875 :end 9109 :pre-blank 1 :contents-begin 8898 :contents-end 9109 :robust-begin 8900 :robust-end 9107 :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 8875 :title (#("Can't run a module" 0 18 (:parent #191))) :mode nil :granularity nil :parent #186) (section (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :robust-begin 8898 :robust-end 9107 :post-blank 0 :post-affiliated 8898 :mode section :granularity nil :parent #191) (paragraph (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :post-blank 0 :post-affiliated 8898 :mode planning :granularity nil :parent #194) #("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 #197))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 9109 :end 9610 :pre-blank 1 :contents-begin 9141 :contents-end 9609 :robust-begin 9143 :robust-end 9607 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9109 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #192))) :mode nil :granularity nil :parent #186) (section (:begin 9141 :end 9610 :contents-begin 9141 :contents-end 9609 :robust-begin 9141 :robust-end 9607 :post-blank 1 :post-affiliated 9141 :mode section :granularity nil :parent #192) (paragraph (:begin 9141 :end 9153 :contents-begin 9141 :contents-end 9152 :post-blank 1 :post-affiliated 9141 :mode planning :granularity nil :parent #195) #("This error\n" 0 11 (:parent #198))) (fixed-width (:begin 9153 :end 9233 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 9153 :mode nil :granularity nil :parent #195)) (paragraph (:begin 9233 :end 9364 :contents-begin 9233 :contents-end 9363 :post-blank 1 :post-affiliated 9233 :mode nil :granularity nil :parent #195) #("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 #200))) (paragraph (:begin 9364 :end 9609 :contents-begin 9364 :contents-end 9609 :post-blank 0 :post-affiliated 9364 :mode nil :granularity nil :parent #195) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #201)) (subscript (:begin 9427 :end 9432 :use-brackets-p nil :contents-begin 9428 :contents-end 9432 :post-blank 0 :parent #201) #("LIBS" 0 4 (:parent #205))) (subscript (:begin 9432 :end 9437 :use-brackets-p nil :contents-begin 9433 :contents-end 9437 :post-blank 0 :parent #201) #("SITE" 0 4 (:parent #206))) #(". 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 #201))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 9610 :end 10276 :pre-blank 1 :contents-begin 9662 :contents-end 10274 :robust-begin 9664 :robust-end 10272 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9610 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #193))) :mode nil :granularity nil :parent #186) (section (:begin 9662 :end 10276 :contents-begin 9662 :contents-end 10274 :robust-begin 9662 :robust-end 10272 :post-blank 2 :post-affiliated 9662 :mode section :granularity nil :parent #193) (paragraph (:begin 9662 :end 9683 :contents-begin 9662 :contents-end 9682 :post-blank 1 :post-affiliated 9662 :mode planning :granularity nil :parent #196) #("The following error\n" 0 20 (:parent #199))) (fixed-width (:begin 9683 :end 9878 :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 9683 :mode nil :granularity nil :parent #196)) (paragraph (:begin 9878 :end 10036 :contents-begin 9878 :contents-end 10035 :post-blank 1 :post-affiliated 9878 :mode nil :granularity nil :parent #196) #("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 #201))) (fixed-width (:begin 10036 :end 10058 :value "mysql -h localhost" :post-blank 2 :post-affiliated 10036 :mode nil :granularity nil :parent #196)) (paragraph (:begin 10058 :end 10115 :contents-begin 10058 :contents-end 10114 :post-blank 1 :post-affiliated 10058 :mode nil :granularity nil :parent #196) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #203))) (fixed-width (:begin 10115 :end 10137 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 10115 :mode nil :granularity nil :parent #196)) (paragraph (:begin 10137 :end 10208 :contents-begin 10137 :contents-end 10207 :post-blank 1 :post-affiliated 10137 :mode nil :granularity nil :parent #196) #("if that works run genenetwork after setting SQL" 0 47 (:parent #205)) (subscript (:begin 10184 :end 10189 :use-brackets-p nil :contents-begin 10185 :contents-end 10188 :post-blank 1 :parent #205) #("URI" 0 3 (:parent #209))) #("to something like\n" 0 18 (:parent #205))) (fixed-width (:begin 10208 :end 10274 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 10208 :mode nil :granularity nil :parent #196))))) (headline (:raw-value "IRC session" :begin 10276 :end 14428 :pre-blank 1 :contents-begin 10291 :contents-end 14428 :robust-begin 10293 :robust-end 14426 :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 10276 :title (#("IRC session" 0 11 (:parent #187))) :mode nil :granularity nil :parent #173) (section (:begin 10291 :end 14428 :contents-begin 10291 :contents-end 14428 :robust-begin 10291 :robust-end 14426 :post-blank 0 :post-affiliated 10291 :mode section :granularity nil :parent #187) (paragraph (:begin 10291 :end 10400 :contents-begin 10291 :contents-end 10399 :post-blank 1 :post-affiliated 10291 :mode planning :granularity nil :parent #190) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #193))) (paragraph (:begin 10400 :end 10961 :contents-begin 10400 :contents-end 10960 :post-blank 1 :post-affiliated 10400 :mode nil :granularity nil :parent #190) #("#+begin" 0 7 (:parent #194)) (subscript (:begin 10407 :end 10411 :use-brackets-p nil :contents-begin 10408 :contents-end 10411 :post-blank 0 :parent #194) #("src" 0 3 (:parent #198))) #("\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 #194))) (paragraph (:begin 10961 :end 11051 :contents-begin 10961 :contents-end 11050 :post-blank 1 :post-affiliated 10961 :mode nil :granularity nil :parent #190) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #195))) (paragraph (:begin 11051 :end 11196 :contents-begin 11051 :contents-end 11195 :post-blank 1 :post-affiliated 11051 :mode nil :granularity nil :parent #190) #(" yes\n env GUIX" 0 30 (:parent #196)) (subscript (:begin 11081 :end 11089 :use-brackets-p nil :contents-begin 11082 :contents-end 11089 :post-blank 0 :parent #196) #("PACKAGE" 0 7 (:parent #200))) (subscript (:begin 11089 :end 11094 :use-brackets-p nil :contents-begin 11090 :contents-end 11094 :post-blank 0 :parent #196) #("PATH" 0 4 (:parent #201))) #("=../guix-bioinformatics ./pre-inst-env guix\n package -A genenetwork2 [07:08]\n shows\n" 0 101 (:parent #196))) (paragraph (:begin 11196 :end 11492 :contents-begin 11196 :contents-end 11491 :post-blank 1 :post-affiliated 11196 :mode nil :granularity nil :parent #190) #("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 #197))) (paragraph (:begin 11492 :end 12685 :contents-begin 11492 :contents-end 12684 :post-blank 1 :post-affiliated 11492 :mode nil :granularity nil :parent #190) #(" 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 #198)) (subscript (:begin 12245 :end 12253 :use-brackets-p nil :contents-begin 12246 :contents-end 12253 :post-blank 0 :parent #198) #("PACKAGE" 0 7 (:parent #202))) (subscript (:begin 12253 :end 12258 :use-brackets-p nil :contents-begin 12254 :contents-end 12258 :post-blank 0 :parent #198) #("PATH" 0 4 (:parent #203))) #("=../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 #198))) (paragraph (:begin 12685 :end 12889 :contents-begin 12685 :contents-end 12888 :post-blank 1 :post-affiliated 12685 :mode nil :granularity nil :parent #190) #("/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 #199))) (paragraph (:begin 12889 :end 14428 :contents-begin 12889 :contents-end 14428 :post-blank 0 :post-affiliated 12889 :mode nil :granularity nil :parent #190) #(" which should have the same HASH values " 0 48 (:parent #200)) (italic (:begin 12937 :end 13846 :post-blank 0 :contents-begin 12938 :contents-end 13845 :parent #200) #("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 #204))) #(".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" 0 582 (:parent #200))))))) #103)) #79)) #47 (item (:bullet "- " :begin 156 :end 268 :contents-begin 159 :contents-end 268 :checkbox nil :counter nil :structure ((121 1 "- " nil nil 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:mode first-section :granularity nil :parent #151) (keyword (:key "TITLE" :value "Installing GeneNetwork services" :begin 1 :end 42 :post-blank 0 :post-affiliated 1 :mode top-comment :granularity nil :parent #154))) #105 (headline (:raw-value "Introduction" :begin 1312 :end 2200 :pre-blank 1 :contents-begin 1328 :contents-end 2199 :robust-begin 1330 :robust-end 2197 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 1312 :title (#("Introduction" 0 12 (:parent #156))) :mode nil :granularity nil :parent #151) (section (:begin 1328 :end 2200 :contents-begin 1328 :contents-end 2199 :robust-begin 1328 :robust-end 2197 :post-blank 1 :post-affiliated 1328 :mode section :granularity nil :parent #156) (paragraph (:begin 1328 :end 1714 :contents-begin 1328 :contents-end 1713 :post-blank 1 :post-affiliated 1328 :mode planning :granularity nil :parent #159) #("Large system deployments can get very 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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 #162)) (link (:type "https" :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil :begin 1557 :end 1631 :contents-begin 1619 :contents-end 1629 :post-blank 0 :parent #162) #("Guix-notes" 0 10 (:parent #168))) #("). The Guix\nsystem can be used to install GN with all its files and dependencies.\n" 0 82 (:parent #162))) (paragraph (:begin 1714 :end 2064 :contents-begin 1714 :contents-end 2063 :post-blank 1 :post-affiliated 1714 :mode nil :granularity nil :parent #159) #("The official installation path is from a checked out version of the\nmain Guix package tree and that of the Genenetwork package\ntree. Current supported versions can be found as the SHA values of\n'gn-latest' branches of " 0 218 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix-bioinformatics" :format bracket :raw-link "https://gitlab.com/genenetwork/guix-bioinformatics" :application nil :search-option nil :begin 1932 :end 2008 :contents-begin 1986 :contents-end 2005 :post-blank 1 :parent #163) #("Guix bioinformatics" 0 19 (:parent #167))) #("and " 0 4 (:parent #163)) (link (:type "https" :path "//gitlab.com/genenetwork/guix" :format bracket :raw-link "https://gitlab.com/genenetwork/guix" :application nil :search-option nil :begin 2012 :end 2061 :contents-begin 2051 :contents-end 2059 :post-blank 0 :parent #163) #("GNU Guix" 0 8 (:parent #169))) #(".\n" 0 2 (:parent #163))) (paragraph (:begin 2064 :end 2199 :contents-begin 2064 :contents-end 2199 :post-blank 0 :post-affiliated 2064 :mode nil :granularity nil :parent #159) #("For a full view of runtime dependencies as defined by GNU Guix, see\nan example of the " 0 86 (:parent #164)) (link (:type "custom-id" :path "gn2-dependency-graph" :format bracket :raw-link "#gn2-dependency-graph" :application nil :search-option nil :begin 2150 :end 2197 :contents-begin 2175 :contents-end 2195 :post-blank 0 :parent #164) #("GN2 Dependency Graph" 0 20 (:parent #168))) #(".\n" 0 2 (:parent #164))))) (headline (:raw-value "Install" :begin 2200 :end 3583 :pre-blank 1 :contents-begin 2211 :contents-end 3582 :robust-begin 2213 :robust-end 3580 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2200 :title (#("Install" 0 7 (:parent #157))) :mode nil :granularity nil :parent #151) (section (:begin 2211 :end 2575 :contents-begin 2211 :contents-end 2574 :robust-begin 2211 :robust-end 2572 :post-blank 1 :post-affiliated 2211 :mode section :granularity nil :parent #157) (paragraph (:begin 2211 :end 2574 :contents-begin 2211 :contents-end 2574 :post-blank 0 :post-affiliated 2211 :mode planning :granularity nil :parent #160) #("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 #163)))) (headline (:raw-value "Tarball" :begin 2575 :end 3228 :pre-blank 1 :contents-begin 2587 :contents-end 3227 :robust-begin 2589 :robust-end 3225 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 2575 :title (#("Tarball" 0 7 (:parent #161))) :mode nil :granularity nil :parent #157) (section (:begin 2587 :end 3228 :contents-begin 2587 :contents-end 3227 :robust-begin 2587 :robust-end 3225 :post-blank 1 :post-affiliated 2587 :mode section :granularity nil :parent #161) (paragraph (:begin 2587 :end 2734 :contents-begin 2587 :contents-end 2733 :post-blank 1 :post-affiliated 2587 :mode planning :granularity nil :parent #164) #("Download the ~800Mb tarball from\n" 0 33 (:parent #167)) (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 2620 :end 2677 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(". Validate the checksum and\nunpack to root, for example\n" 0 56 (:parent #167))) (fixed-width (:begin 2734 :end 2836 :value "tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz\nmv /gnu /\nmv /opt/genenetwork2 /opt/" :post-blank 2 :post-affiliated 2734 :mode nil :granularity nil :parent #164)) (paragraph (:begin 2836 :end 2884 :contents-begin 2836 :contents-end 2883 :post-blank 1 :post-affiliated 2836 :mode nil :granularity nil :parent #164) #("Now you shoud be able to start the server with\n" 0 47 (:parent #169))) (fixed-width (:begin 2884 :end 2922 :value "/opt/genenetwork2/bin/genenetwork2" :post-blank 2 :post-affiliated 2884 :mode nil :granularity nil :parent #164)) (paragraph (:begin 2922 :end 3049 :contents-begin 2922 :contents-end 3048 :post-blank 1 :post-affiliated 2922 :mode nil :granularity nil :parent #164) #("When the server stops with a MySQL error " 0 41 (:parent #171)) (link (:type "custom-id" :path "run-mysql-server" :format bracket :raw-link "#run-mysql-server" :application nil :search-option nil :begin 2963 :end 3002 :contents-begin 2984 :contents-end 3000 :post-blank 0 :parent #171) #("Run MySQL server" 0 16 (:parent #175))) #("\nand set SQL" 0 12 (:parent #171)) (subscript (:begin 3014 :end 3019 :use-brackets-p nil :contents-begin 3015 :contents-end 3018 :post-blank 1 :parent #171) #("URI" 0 3 (:parent #177))) #("to point at it. For example:\n" 0 29 (:parent #171))) (fixed-width (:begin 3049 :end 3116 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 2 :post-affiliated 3049 :mode nil :granularity nil :parent #164)) (paragraph (:begin 3116 :end 3227 :contents-begin 3116 :contents-end 3227 :post-blank 0 :post-affiliated 3116 :mode nil :granularity nil :parent #164) #("See also " 0 9 (:parent #173)) (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 3125 :end 3225 :contents-begin 3176 :contents-end 3223 :post-blank 0 :parent #173) #("Mysql can't connect server through socket ERROR" 0 47 (:parent #177))) #(".\n" 0 2 (:parent #173))))) (headline (:raw-value "Docker" :begin 3228 :end 3437 :pre-blank 1 :contents-begin 3239 :contents-end 3436 :robust-begin 3241 :robust-end 3434 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3228 :title (#("Docker" 0 6 (:parent #162))) :mode nil :granularity nil :parent #157) (section (:begin 3239 :end 3437 :contents-begin 3239 :contents-end 3436 :robust-begin 3239 :robust-end 3434 :post-blank 1 :post-affiliated 3239 :mode section :granularity nil :parent #162) (paragraph (:begin 3239 :end 3436 :contents-begin 3239 :contents-end 3436 :post-blank 0 :post-affiliated 3239 :mode planning :granularity nil :parent #165) #("Docker images are also available through\n" 0 41 (:parent #168)) (link (:type "http" :path "//files.genenetwork.org/software/" :format bracket :raw-link "http://files.genenetwork.org/software/" :application nil :search-option nil :begin 3280 :end 3322 :contents-begin nil :contents-end nil :post-blank 0 :parent #168)) #(". Validate the checksum and run\nwith " 0 37 (:parent #168)) (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 3359 :end 3434 :contents-begin 3421 :contents-end 3432 :post-blank 0 :parent #168) #("Docker load" 0 11 (:parent #174))) #(".\n" 0 2 (:parent #168))))) (headline (:raw-value "With source" :begin 3437 :end 3583 :pre-blank 1 :contents-begin 3453 :contents-end 3582 :robust-begin 3455 :robust-end 3580 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3437 :title (#("With source" 0 11 (:parent #163))) :mode nil :granularity nil :parent #157) (section (:begin 3453 :end 3583 :contents-begin 3453 :contents-end 3582 :robust-begin 3453 :robust-end 3580 :post-blank 1 :post-affiliated 3453 :mode section :granularity nil :parent #163) (paragraph (:begin 3453 :end 3582 :contents-begin 3453 :contents-end 3582 :post-blank 0 :post-affiliated 3453 :mode planning :granularity nil :parent #166) #("For more elaborate installation instructions on deploying GeneNetwork from\nsource see " 0 86 (:parent #169)) (link (:type "custom-id" :path "source-deployment" :format bracket :raw-link "#source-deployment" :application nil :search-option nil :begin 3539 :end 3580 :contents-begin 3561 :contents-end 3578 :post-blank 0 :parent #169) #("Source deployment" 0 17 (:parent #173))) #(".\n" 0 2 (:parent #169)))))) (headline (:raw-value "Running GN2" :begin 3583 :end 4064 :pre-blank 1 :contents-begin 3598 :contents-end 4063 :robust-begin 3600 :robust-end 4061 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 3583 :title (#("Running GN2" 0 11 (:parent #158))) :mode nil :granularity nil :parent #151) (section (:begin 3598 :end 4064 :contents-begin 3598 :contents-end 4063 :robust-begin 3598 :robust-end 4061 :post-blank 1 :post-affiliated 3598 :mode section :granularity nil :parent #158) (paragraph (:begin 3598 :end 3793 :contents-begin 3598 :contents-end 3792 :post-blank 1 :post-affiliated 3598 :mode planning :granularity nil :parent #161) #("Default settings for GN2 are listed in a file called\n" 0 53 (:parent #164)) (link (:type "file" :path "../etc/default_settings.py" :format bracket :raw-link "../etc/default_settings.py" :application nil :search-option nil :begin 3651 :end 3702 :contents-begin 3681 :contents-end 3700 :post-blank 0 :parent #164) #("default" 0 7 (:parent #168)) (subscript (:begin 3688 :end 3700 :use-brackets-p nil :contents-begin 3689 :contents-end 3700 :post-blank 0 :parent #168) #("settings.py" 0 11 (:parent #172)))) #(". You can copy this file and pass it as a new\nparameter to the genenetwork2 command, e.g.\n" 0 90 (:parent #164))) (fixed-width (:begin 3793 :end 3823 :value "genenetwork2 mysettings.py" :post-blank 2 :post-affiliated 3793 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3823 :end 3901 :contents-begin 3823 :contents-end 3900 :post-blank 1 :post-affiliated 3823 :mode nil :granularity nil :parent #161) #("or you can set environment variables to override individual parameters, e.g.\n" 0 77 (:parent #166))) (fixed-width (:begin 3901 :end 3984 :value "env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2" :post-blank 2 :post-affiliated 3901 :mode nil :granularity nil :parent #161)) (paragraph (:begin 3984 :end 4063 :contents-begin 3984 :contents-end 4063 :post-blank 0 :post-affiliated 3984 :mode nil :granularity nil :parent #161) #("the debug and logging switches can be particularly useful when\ndeveloping GN2.\n" 0 79 (:parent #168))))) (headline (:raw-value "Run MySQL server" :begin 4064 :end 6699 :pre-blank 0 :contents-begin 4083 :contents-end 6698 :robust-begin 4085 :robust-end 6696 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4064 :title (#("Run MySQL server" 0 16 (:parent #159))) :mode nil :granularity nil :parent #151) (headline (:raw-value "Install MySQL with GNU GUIx" :begin 4083 :end 5167 :pre-blank 1 :contents-begin 4115 :contents-end 5166 :robust-begin 4117 :robust-end 5164 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 4083 :title (#("Install MySQL with GNU GUIx" 0 27 (:parent #162))) :mode section :granularity nil :parent #159) (section (:begin 4115 :end 5167 :contents-begin 4115 :contents-end 5166 :robust-begin 4115 :robust-end 5164 :post-blank 1 :post-affiliated 4115 :mode section :granularity nil :parent #162) (paragraph (:begin 4115 :end 4250 :contents-begin 4115 :contents-end 4249 :post-blank 1 :post-affiliated 4115 :mode planning :granularity nil :parent #165) #("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 #168))) (paragraph (:begin 4250 :end 4277 :contents-begin 4250 :contents-end 4276 :post-blank 1 :post-affiliated 4250 :mode nil :granularity nil :parent #165) #("As root configure and run\n" 0 26 (:parent #169))) (src-block (:language "bash" :switches nil :parameters nil :begin 4277 :end 4535 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "adduser mysql && addgroup mysql\nmysqld --datadir=/var/mysql --initialize-insecure\nmkdir -p /var/run/mysqld\nchown mysql.mysql ~/mysql /var/run/mysqld\nmysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048\"\n" :post-blank 1 :post-affiliated 4277 :mode nil :granularity nil :parent #165)) (paragraph (:begin 4535 :end 4583 :contents-begin 4535 :contents-end 4582 :post-blank 1 :post-affiliated 4535 :mode nil :granularity nil :parent #165) #("If you want to run as root you may have to set\n" 0 47 (:parent #171))) (fixed-width (:begin 4583 :end 4621 :value "/etc/my.cnf\n[mysqld]\nuser=root" :post-blank 2 :post-affiliated 4583 :mode nil :granularity nil :parent #165)) (paragraph (:begin 4621 :end 4690 :contents-begin 4621 :contents-end 4689 :post-blank 1 :post-affiliated 4621 :mode nil :granularity nil :parent #165) #("To check error output in a file on start-up run with something like\n" 0 68 (:parent #173))) (fixed-width (:begin 4690 :end 4799 :value "mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log" :post-blank 2 :post-affiliated 4690 :mode nil :granularity nil :parent #165)) (paragraph (:begin 4799 :end 4875 :contents-begin 4799 :contents-end 4874 :post-blank 1 :post-affiliated 4799 :mode nil :granularity nil :parent #165) #("Other tips are that Guix installs mysqld in your profile, so this may work\n" 0 75 (:parent #175))) (fixed-width (:begin 4875 :end 4979 :value "/home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql" :post-blank 2 :post-affiliated 4875 :mode nil :granularity nil :parent #165)) (paragraph (:begin 4979 :end 5006 :contents-begin 4979 :contents-end 5005 :post-blank 1 :post-affiliated 4979 :mode nil :granularity nil :parent #165) #("When you get errors like:\n" 0 26 (:parent #177))) (fixed-width (:begin 5006 :end 5118 :value "qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint')" :post-blank 2 :post-affiliated 5006 :mode nil :granularity nil :parent #165)) (paragraph (:begin 5118 :end 5139 :contents-begin 5118 :contents-end 5138 :post-blank 1 :post-affiliated 5118 :mode nil :granularity nil :parent #165) #("you may need to set\n" 0 20 (:parent #179))) (fixed-width (:begin 5139 :end 5166 :value "set foreign_key_checks=0" :post-blank 1 :post-affiliated 5139 :mode nil :granularity nil :parent #165)))) (headline (:raw-value "Load the small database in MySQL" :begin 5167 :end 6699 :pre-blank 1 :contents-begin 5204 :contents-end 6698 :robust-begin 5206 :robust-end 6696 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5167 :title (#("Load the small database in MySQL" 0 32 (:parent #163))) :mode nil :granularity nil :parent #159) (section (:begin 5204 :end 6699 :contents-begin 5204 :contents-end 6698 :robust-begin 5204 :robust-end 6696 :post-blank 1 :post-affiliated 5204 :mode section :granularity nil :parent #163) (paragraph (:begin 5204 :end 5511 :contents-begin 5204 :contents-end 5510 :post-blank 1 :post-affiliated 5204 :mode planning :granularity nil :parent #166) #("At this point we require the underlying distribution to install and\nrun mysqld (see next section for GNU Guix). Currently we have two databases for deployment,\n'db" 0 163 (:parent #169)) (subscript (:begin 5367 :end 5374 :use-brackets-p nil :contents-begin 5368 :contents-end 5374 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #173))) (subscript (:begin 5374 :end 5376 :use-brackets-p nil :contents-begin 5375 :contents-end 5376 :post-blank 0 :parent #169) #("s" 0 1 (:parent #174))) #("' is the small testing database containing experiments\nfrom BXD mice and 'db" 0 76 (:parent #169)) (subscript (:begin 5452 :end 5459 :use-brackets-p nil :contents-begin 5453 :contents-end 5459 :post-blank 0 :parent #169) #("webqtl" 0 6 (:parent #176))) (subscript (:begin 5459 :end 5465 :use-brackets-p nil :contents-begin 5460 :contents-end 5465 :post-blank 0 :parent #169) #("plant" 0 5 (:parent #177))) #("' which contains all plant related\nmaterial.\n" 0 45 (:parent #169))) (paragraph (:begin 5511 :end 5539 :contents-begin 5511 :contents-end 5538 :post-blank 1 :post-affiliated 5511 :mode nil :granularity nil :parent #166) #("Download one database from\n" 0 27 (:parent #170))) (paragraph (:begin 5539 :end 5587 :contents-begin 5539 :contents-end 5586 :post-blank 1 :post-affiliated 5539 :mode nil :granularity nil :parent #166) (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 5539 :end 5585 :contents-begin nil :contents-end nil :post-blank 0 :parent #171)) #("\n" 0 1 (:parent #171))) (paragraph (:begin 5587 :end 5646 :contents-begin 5587 :contents-end 5645 :post-blank 1 :post-affiliated 5587 :mode nil :granularity nil :parent #166) (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 5587 :end 5644 :contents-begin nil :contents-end nil :post-blank 0 :parent #172)) #("\n" 0 1 (:parent #172))) (paragraph (:begin 5646 :end 5665 :contents-begin 5646 :contents-end 5664 :post-blank 1 :post-affiliated 5646 :mode nil :granularity nil :parent #166) #("Check the md5sum.\n" 0 18 (:parent #173))) (paragraph (:begin 5665 :end 5736 :contents-begin 5665 :contents-end 5735 :post-blank 1 :post-affiliated 5665 :mode nil :granularity nil :parent #166) #("After installation inflate the database binary in the MySQL directory\n" 0 70 (:parent #174))) (fixed-width (:begin 5736 :end 5837 :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 5736 :mode nil :granularity nil :parent #166)) (paragraph (:begin 5837 :end 5884 :contents-begin 5837 :contents-end 5883 :post-blank 1 :post-affiliated 5837 :mode nil :granularity nil :parent #166) #("restart MySQL service (mysqld). Login as root\n" 0 46 (:parent #176))) (fixed-width (:begin 5884 :end 5901 :value "myslq -u root" :post-blank 2 :post-affiliated 5884 :mode nil :granularity nil :parent #166)) (paragraph (:begin 5901 :end 5906 :contents-begin 5901 :contents-end 5905 :post-blank 1 :post-affiliated 5901 :mode nil :granularity nil :parent #166) #("and\n" 0 4 (:parent #178))) (fixed-width (:begin 5906 :end 6132 :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 5906 :mode nil :granularity nil :parent #166)) (paragraph (:begin 6132 :end 6197 :contents-begin 6132 :contents-end 6196 :post-blank 1 :post-affiliated 6132 :mode nil :granularity nil :parent #166) #("Set permissions and match password in your settings file below:\n" 0 64 (:parent #180))) (fixed-width (:begin 6197 :end 6296 :value "mysql> grant all privileges on db_webqtl_s.* to gn2@\"localhost\" identified by 'mysql_password';" :post-blank 2 :post-affiliated 6197 :mode nil :granularity nil :parent #166)) (paragraph (:begin 6296 :end 6403 :contents-begin 6296 :contents-end 6402 :post-blank 1 :post-affiliated 6296 :mode nil :granularity nil :parent #166) #("You may need to change \"localhost\" to whatever domain you are\nconnecting from (mysql will give an error).\n" 0 106 (:parent #182))) (paragraph (:begin 6403 :end 6566 :contents-begin 6403 :contents-end 6565 :post-blank 1 :post-affiliated 6403 :mode nil :granularity nil :parent #166) #("Note that if the mysql connection is not working, try connecting to\nthe IP address and check server firewall, hosts.allow and mysql IP\nconfiguration (see below).\n" 0 162 (:parent #183))) (paragraph (:begin 6566 :end 6698 :contents-begin 6566 :contents-end 6698 :post-blank 0 :post-affiliated 6566 :mode nil :granularity nil :parent #166) #("Note for the plant database you can rename it to db" 0 51 (:parent #184)) (subscript (:begin 6617 :end 6624 :use-brackets-p nil :contents-begin 6618 :contents-end 6624 :post-blank 0 :parent #184) #("webqtl" 0 6 (:parent #188))) (subscript (:begin 6624 :end 6626 :use-brackets-p nil :contents-begin 6625 :contents-end 6626 :post-blank 0 :parent #184) #("s" 0 1 (:parent #189))) #(", or\nchange the settings in etc/default" 0 39 (:parent #184)) (subscript (:begin 6665 :end 6678 :use-brackets-p nil :contents-begin 6666 :contents-end 6677 :post-blank 1 :parent #184) #("settings.py" 0 11 (:parent #191))) #("to match your path.\n" 0 20 (:parent #184)))))) (headline (:raw-value "GN2 Dependency Graph" :begin 6699 :end 6863 :pre-blank 1 :contents-begin 6723 :contents-end 6862 :robust-begin 6725 :robust-end 6860 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6699 :title (#("GN2 Dependency Graph" 0 20 (:parent #160))) :mode nil :granularity nil :parent #151) (section (:begin 6723 :end 6863 :contents-begin 6723 :contents-end 6862 :robust-begin 6723 :robust-end 6860 :post-blank 1 :post-affiliated 6723 :mode section :granularity nil :parent #160) (paragraph (:begin 6723 :end 6784 :contents-begin 6723 :contents-end 6783 :post-blank 1 :post-affiliated 6723 :mode planning :granularity nil :parent #163) #("Graph of all runtime dependencies as installed by GNU Guix.\n" 0 60 (:parent #166))) (paragraph (:begin 6784 :end 6862 :contents-begin 6814 :contents-end 6862 :post-blank 0 :post-affiliated 6814 :attr_html (":title GN2_graph") :mode nil :granularity nil :parent #163) (link (:type "http" :path "//biogems.info/contrib/genenetwork/gn2.svg" :format plain :raw-link "http://biogems.info/contrib/genenetwork/gn2.svg" :application nil :search-option nil :begin 6814 :end 6861 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #("\n" 0 1 (:parent #167))))) (headline (:raw-value "Working with the GN2 source code" :begin 6863 :end 6925 :pre-blank 1 :contents-begin 6899 :contents-end 6924 :robust-begin 6901 :robust-end 6922 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6863 :title (#("Working with the GN2 source code" 0 32 (:parent #161))) :mode nil :granularity nil :parent #151) (section (:begin 6899 :end 6925 :contents-begin 6899 :contents-end 6924 :robust-begin 6899 :robust-end 6922 :post-blank 1 :post-affiliated 6899 :mode section :granularity nil :parent #161) (paragraph (:begin 6899 :end 6924 :contents-begin 6899 :contents-end 6924 :post-blank 0 :post-affiliated 6899 :mode planning :granularity nil :parent #164) #("See " 0 4 (:parent #167)) (link (:type "fuzzy" :path "development.org" :format bracket :raw-link "development.org" :application nil :search-option nil :begin 6903 :end 6922 :contents-begin nil :contents-end nil :post-blank 0 :parent #167)) #(".\n" 0 2 (:parent #167))))) (headline (:raw-value "Running ElasticSearch" :begin 6925 :end 7675 :pre-blank 1 :contents-begin 6950 :contents-end 7674 :robust-begin 6952 :robust-end 7672 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 6925 :title (#("Running ElasticSearch" 0 21 (:parent #162))) :parent #151 :cached t :granularity nil) (section (:begin 6950 :end 7134 :contents-begin 6950 :contents-end 7132 :robust-begin 6950 :robust-end 7130 :post-blank 2 :post-affiliated 6950 :mode section :granularity nil :parent #162) (paragraph (:begin 6950 :end 7132 :contents-begin 6950 :contents-end 7132 :post-blank 0 :post-affiliated 6950 :mode planning :granularity nil :parent #165) #("In order to start up elasticsearch:\nPenguin - change user to \"elasticsearch\" and use the following command: \"env JAVA" 0 117 (:parent #168)) (subscript (:begin 7067 :end 7072 :use-brackets-p nil :contents-begin 7068 :contents-end 7072 :post-blank 0 :parent #168) #("HOME" 0 4 (:parent #172))) #("=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch\"\n" 0 60 (:parent #168)))) (headline (:raw-value "SystemD" :begin 7134 :end 7675 :pre-blank 1 :contents-begin 7146 :contents-end 7674 :robust-begin 7148 :robust-end 7672 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7134 :title (#("SystemD" 0 7 (:parent #166))) :parent #162 :cached t :org-element--cache-sync-key (1 . 7134) :granularity nil) (section (:begin 7146 :end 7675 :contents-begin 7146 :contents-end 7674 :robust-begin 7146 :robust-end 7672 :post-blank 1 :post-affiliated 7146 :mode section :granularity nil :parent #166) (paragraph (:begin 7146 :end 7206 :contents-begin 7146 :contents-end 7205 :post-blank 1 :post-affiliated 7146 :mode planning :granularity nil :parent #169) #("New server - as root run \"systemctl restart elasticsearch\"\n" 0 59 (:parent #172))) (src-block (:language nil :switches nil :parameters nil :begin 7206 :end 7674 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "tux01:/etc/systemd/system# cat elasticsearch.service\n[Unit]\nDescription=Run Elasticsearch\n\n[Service]\nExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch\nEnvironment=JAVA_HOME=/opt/jdk-9.0.4\nEnvironment=\"ES_JAVA_OPTS=-Xms1g -Xmx8g\"\nEnvironment=\"PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin\"\nLimitNOFILE=65536\nStandardOutput=syslog\nStandardError=syslog\nUser=elasticsearch\n\n[Install]\nWantedBy=multi-user.target\n" :post-blank 0 :post-affiliated 7206 :mode nil :granularity nil :parent #169))))) (headline (:raw-value "Read more" :begin 7675 :end 7825 :pre-blank 1 :contents-begin 7688 :contents-end 7824 :robust-begin 7690 :robust-end 7822 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7675 :title (#("Read more" 0 9 (:parent #163))) :mode nil :granularity nil :parent #151) (section (:begin 7688 :end 7825 :contents-begin 7688 :contents-end 7824 :robust-begin 7688 :robust-end 7822 :post-blank 1 :post-affiliated 7688 :mode section :granularity nil :parent #163) (paragraph (:begin 7688 :end 7824 :contents-begin 7688 :contents-end 7824 :post-blank 0 :post-affiliated 7688 :mode planning :granularity nil :parent #166) #("If you want to understand the architecture of GN2 read\n" 0 55 (:parent #169)) (link (:type "fuzzy" :path "Architecture.org" :format bracket :raw-link "Architecture.org" :application nil :search-option nil :begin 7743 :end 7763 :contents-begin nil :contents-end nil :post-blank 0 :parent #169)) #(". The rest of this document is mostly on deployment\nof GN2.\n" 0 61 (:parent #169))))) (headline (:raw-value "Trouble shooting" :begin 7825 :end 10276 :pre-blank 1 :contents-begin 7845 :contents-end 10274 :robust-begin 7847 :robust-end 10272 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 7825 :title (#("Trouble shooting" 0 16 (:parent #164))) :mode nil :granularity nil :parent #151) (headline (:raw-value "ImportError: No module named jinja2" :begin 7845 :end 8379 :pre-blank 1 :contents-begin 7885 :contents-end 8379 :robust-begin 7887 :robust-end 8377 :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 7845 :title (#("ImportError: No module named jinja2" 0 35 (:parent #167))) :mode section :granularity nil :parent #164) (section (:begin 7885 :end 8379 :contents-begin 7885 :contents-end 8379 :robust-begin 7885 :robust-end 8377 :post-blank 0 :post-affiliated 7885 :mode section :granularity nil :parent #167) (paragraph (:begin 7885 :end 8120 :contents-begin 7885 :contents-end 8119 :post-blank 1 :post-affiliated 7885 :mode planning :granularity nil :parent #170) #("If you have all the Guix packages installed this error points out that\nthe environment variables are not set. Copy-paste the paths into your\nterminal (mainly so PYTHON" 0 167 (:parent #173)) (subscript (:begin 8052 :end 8058 :use-brackets-p nil :contents-begin 8053 :contents-end 8057 :post-blank 1 :parent #173) #("PATH" 0 4 (:parent #177))) #("and R" 0 5 (:parent #173)) (subscript (:begin 8063 :end 8068 :use-brackets-p nil :contents-begin 8064 :contents-end 8068 :post-blank 0 :parent #173) #("LIBS" 0 4 (:parent #179))) (subscript (:begin 8068 :end 8074 :use-brackets-p nil :contents-begin 8069 :contents-end 8073 :post-blank 1 :parent #173) #("SITE" 0 4 (:parent #180))) #("are set) from the\ninformation given by guix:\n" 0 45 (:parent #173))) (fixed-width (:begin 8120 :end 8151 :value "guix package --search-paths" :post-blank 2 :post-affiliated 8120 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8151 :end 8167 :contents-begin 8151 :contents-end 8166 :post-blank 1 :post-affiliated 8151 :mode nil :granularity nil :parent #170) #("On one system:\n" 0 15 (:parent #175))) (fixed-width (:begin 8167 :end 8355 :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 8167 :mode nil :granularity nil :parent #170)) (paragraph (:begin 8355 :end 8379 :contents-begin 8355 :contents-end 8379 :post-blank 0 :post-affiliated 8355 :mode nil :granularity nil :parent #170) #("and perhaps a few more.\n" 0 24 (:parent #177))))) (headline (:raw-value "ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'" :begin 8379 :end 8875 :pre-blank 1 :contents-begin 8488 :contents-end 8874 :robust-begin 8490 :robust-end 8872 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 8379 :title (#("ERROR: 'can not find directory $HOME/gn2" 0 40 (:parent #168)) (subscript (:begin 8422 :end 8427 :use-brackets-p nil :contents-begin 8423 :contents-end 8427 :post-blank 0 :parent #168) #("data" 0 4 (:parent #210))) #("' or 'can not find directory $HOME/genotype" 0 43 (:parent #168)) (subscript (:begin 8470 :end 8476 :use-brackets-p nil :contents-begin 8471 :contents-end 8476 :post-blank 0 :parent #168) #("files" 0 5 (:parent #212))) #("/genotype'" 0 10 (:parent #168))) :mode nil :granularity nil :parent #164) (section (:begin 8488 :end 8875 :contents-begin 8488 :contents-end 8874 :robust-begin 8488 :robust-end 8872 :post-blank 1 :post-affiliated 8488 :mode section :granularity nil :parent #168) (paragraph (:begin 8488 :end 8710 :contents-begin 8488 :contents-end 8709 :post-blank 1 :post-affiliated 8488 :mode planning :granularity nil :parent #171) #("The default settings file looks in your $HOME/gn2" 0 49 (:parent #174)) (subscript (:begin 8537 :end 8542 :use-brackets-p nil :contents-begin 8538 :contents-end 8542 :post-blank 0 :parent #174) #("data" 0 4 (:parent #178))) #(". Since these\nfiles come with a Guix installation you should take a hint from the\nvalues in the installed version of default" 0 124 (:parent #174)) (subscript (:begin 8666 :end 8679 :use-brackets-p nil :contents-begin 8667 :contents-end 8678 :post-blank 1 :parent #174) #("settings.py" 0 11 (:parent #180))) #("(see above in\nthis document).\n" 0 30 (:parent #174))) (paragraph (:begin 8710 :end 8784 :contents-begin 8710 :contents-end 8783 :post-blank 1 :post-affiliated 8710 :mode nil :granularity nil :parent #171) #("You can use the GENENETWORK" 0 27 (:parent #175)) (subscript (:begin 8737 :end 8744 :use-brackets-p nil :contents-begin 8738 :contents-end 8743 :post-blank 1 :parent #175) #("FILES" 0 5 (:parent #179))) #("switch to set the datadir, for example\n" 0 39 (:parent #175))) (fixed-width (:begin 8784 :end 8874 :value "env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2" :post-blank 1 :post-affiliated 8784 :mode nil :granularity nil :parent #171)))) (headline (:raw-value "Can't run a module" :begin 8875 :end 9109 :pre-blank 1 :contents-begin 8898 :contents-end 9109 :robust-begin 8900 :robust-end 9107 :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 8875 :title (#("Can't run a module" 0 18 (:parent #169))) :mode nil :granularity nil :parent #164) (section (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :robust-begin 8898 :robust-end 9107 :post-blank 0 :post-affiliated 8898 :mode section :granularity nil :parent #169) (paragraph (:begin 8898 :end 9109 :contents-begin 8898 :contents-end 9109 :post-blank 0 :post-affiliated 8898 :mode planning :granularity nil :parent #172) #("In rare cases, development modules are not brought in with Guix\nbecause no source code is available. This can lead to missing modules\non a running server. Please check with the authors when a module\nis missing.\n" 0 211 (:parent #175))))) (headline (:raw-value "Rpy2 error 'show' now found" :begin 9109 :end 9610 :pre-blank 1 :contents-begin 9141 :contents-end 9609 :robust-begin 9143 :robust-end 9607 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9109 :title (#("Rpy2 error 'show' now found" 0 27 (:parent #170))) :mode nil :granularity nil :parent #164) (section (:begin 9141 :end 9610 :contents-begin 9141 :contents-end 9609 :robust-begin 9141 :robust-end 9607 :post-blank 1 :post-affiliated 9141 :mode section :granularity nil :parent #170) (paragraph (:begin 9141 :end 9153 :contents-begin 9141 :contents-end 9152 :post-blank 1 :post-affiliated 9141 :mode planning :granularity nil :parent #173) #("This error\n" 0 11 (:parent #176))) (fixed-width (:begin 9153 :end 9233 :value "__show = rpy2.rinterface.baseenv.get(\"show\")\nLookupError: 'show' not found" :post-blank 2 :post-affiliated 9153 :mode nil :granularity nil :parent #173)) (paragraph (:begin 9233 :end 9364 :contents-begin 9233 :contents-end 9363 :post-blank 1 :post-affiliated 9233 :mode nil :granularity nil :parent #173) #("means that R was updated in your path, and that Rpy2 needs to be\nrecompiled against this R - don't you love informative messages?\n" 0 130 (:parent #178))) (paragraph (:begin 9364 :end 9609 :contents-begin 9364 :contents-end 9609 :post-blank 0 :post-affiliated 9364 :mode nil :granularity nil :parent #173) #("In our case it means that GN's PYTHONPATH is not in sync with\nR" 0 63 (:parent #179)) (subscript (:begin 9427 :end 9432 :use-brackets-p nil :contents-begin 9428 :contents-end 9432 :post-blank 0 :parent #179) #("LIBS" 0 4 (:parent #183))) (subscript (:begin 9432 :end 9437 :use-brackets-p nil :contents-begin 9433 :contents-end 9437 :post-blank 0 :parent #179) #("SITE" 0 4 (:parent #184))) #(". Please check your GNU Guix GN2 installation paths,\nyou man need to reinstall. Note that this may be the point you\nmay want to start using profiles (see profile section).\n" 0 172 (:parent #179))))) (headline (:raw-value "Mysql can't connect server through socket ERROR" :begin 9610 :end 10276 :pre-blank 1 :contents-begin 9662 :contents-end 10274 :robust-begin 9664 :robust-end 10272 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 9610 :title (#("Mysql can't connect server through socket ERROR" 0 47 (:parent #171))) :mode nil :granularity nil :parent #164) (section (:begin 9662 :end 10276 :contents-begin 9662 :contents-end 10274 :robust-begin 9662 :robust-end 10272 :post-blank 2 :post-affiliated 9662 :mode section :granularity nil :parent #171) (paragraph (:begin 9662 :end 9683 :contents-begin 9662 :contents-end 9682 :post-blank 1 :post-affiliated 9662 :mode planning :granularity nil :parent #174) #("The following error\n" 0 20 (:parent #177))) (fixed-width (:begin 9683 :end 9878 :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 9683 :mode nil :granularity nil :parent #174)) (paragraph (:begin 9878 :end 10036 :contents-begin 9878 :contents-end 10035 :post-blank 1 :post-affiliated 9878 :mode nil :granularity nil :parent #174) #("means that MySQL is trying to connect locally to a non-existent MySQL\nserver, something you may see in a container. Typically replicated with something like\n" 0 157 (:parent #179))) (fixed-width (:begin 10036 :end 10058 :value "mysql -h localhost" :post-blank 2 :post-affiliated 10036 :mode nil :granularity nil :parent #174)) (paragraph (:begin 10058 :end 10115 :contents-begin 10058 :contents-end 10114 :post-blank 1 :post-affiliated 10058 :mode nil :granularity nil :parent #174) #("try to connect over the network interface instead, e.g.\n" 0 56 (:parent #181))) (fixed-width (:begin 10115 :end 10137 :value "mysql -h 127.0.0.1" :post-blank 2 :post-affiliated 10115 :mode nil :granularity nil :parent #174)) (paragraph (:begin 10137 :end 10208 :contents-begin 10137 :contents-end 10207 :post-blank 1 :post-affiliated 10137 :mode nil :granularity nil :parent #174) #("if that works run genenetwork after setting SQL" 0 47 (:parent #183)) (subscript (:begin 10184 :end 10189 :use-brackets-p nil :contents-begin 10185 :contents-end 10188 :post-blank 1 :parent #183) #("URI" 0 3 (:parent #187))) #("to something like\n" 0 18 (:parent #183))) (fixed-width (:begin 10208 :end 10274 :value "export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s" :post-blank 1 :post-affiliated 10208 :mode nil :granularity nil :parent #174))))) (headline (:raw-value "IRC session" :begin 10276 :end 14428 :pre-blank 1 :contents-begin 10291 :contents-end 14428 :robust-begin 10293 :robust-end 14426 :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 10276 :title (#("IRC session" 0 11 (:parent #165))) :mode nil :granularity nil :parent #151) (section (:begin 10291 :end 14428 :contents-begin 10291 :contents-end 14428 :robust-begin 10291 :robust-end 14426 :post-blank 0 :post-affiliated 10291 :mode section :granularity nil :parent #165) (paragraph (:begin 10291 :end 10400 :contents-begin 10291 :contents-end 10399 :post-blank 1 :post-affiliated 10291 :mode planning :granularity nil :parent #168) #("Here an IRC session where we installed GN2 from scratch using GNU Guix\nand a download of the test database.\n" 0 108 (:parent #171))) (paragraph (:begin 10400 :end 10961 :contents-begin 10400 :contents-end 10960 :post-blank 1 :post-affiliated 10400 :mode nil :granularity nil :parent #168) #("#+begin" 0 7 (:parent #172)) (subscript (:begin 10407 :end 10411 :use-brackets-p nil :contents-begin 10408 :contents-end 10411 :post-blank 0 :parent #172) #("src" 0 3 (:parent #176))) #("\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 #172))) (paragraph (:begin 10961 :end 11051 :contents-begin 10961 :contents-end 11050 :post-blank 1 :post-affiliated 10961 :mode nil :granularity nil :parent #168) #("Author: David Thompson \nDate: Sun Mar 27 21:20:19 2016 -0400\n" 0 89 (:parent #173))) (paragraph (:begin 11051 :end 11196 :contents-begin 11051 :contents-end 11195 :post-blank 1 :post-affiliated 11051 :mode nil :granularity nil :parent #168) #("
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